Turn Off Your Irony Meters Before Reading This!!!

Back in the days of newsgroups (last century) the howlers in talk.origins developed a running joke about irony meters. They were always being fried by outrageous comments from the anti-science creationists. New, more powerful, irony meters were needed every few months.

The following post appeared on Uncommon Descent today: Is this where science fraud begins?. You are about to read an excerpt but I caution you to turn off your irony meter unless it's a Mark IX (beta) version. Even then, I'm not sure it will survive.

Denyse O'Leary quotes from an article published on Defining Ideas: The Death of Honesty by William Damon.

In July 2011, a widely-reported cheating scandal erupted in school systems in and around Atlanta, Georgia. State investigators found a pattern of “organized and systemic misconduct” dating back for over ten years. One-hundred-and-seventy-eight teachers, and the principals of half of the system’s schools, aided and abetted students who were cheating on their tests. Top administrators ignored news reports of this cheating: a New York Times story described “a culture of fear and intimidation that prevented many teachers from speaking out.”

Nor was this an isolated incident. In a feature on school testing, CBS News reported the following: “New York education officials found 21 proven cases of teacher cheating. Teachers have read off answers during a test, sent students back to correct wrong answers, photocopied secure tests for use in class, inflated scores, and peeked at questions then drilled those topics in class before the test.”

With such prominent and recent instances of cheating among students and teachers today, one would expect a concerted effort to articulate and promote the value of honesty in our schools. Yet school programs regarding academic integrity consist of little more than a patchwork of vaguely-stated prohibitions and half-hearted responses. Our schools vacillate between routine neglect and a circle-the wagons reaction if the problem boils over into a public media scandal. There is little consistency, coherence, or transparency in many school policies.

Let's think about the 178 teachers in schools around Atlanta, Georgia. It's pretty safe to assume that the vast majority of those teachers are god-fearing Christians and most of them don't accept evolution.

So, how does Denyse O'Leary explain why unethical behavior among teachers is so rampant?

The most likely reason is that the educators involved do not believe that anyone has made a free choice to cheat or that cheating is an ethical issue.

Chalk another one up to the high cost of evolutionary psychology and related trends.

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Life: You Know It When You See It

 

Carl Zimmer, who blogs at The Loom, is interested in definitions of life. His latest essay highlights a definition proposed by Edward Trifonov who says that life is: "self-reproduction with variations" [Can A Scientist Define “Life”?].

It didn't take Sean Carroll (the physicist) very long to see one of the main problems with this definition; namely that Sean isn't alive! [Do I Not Live!].

It's true that we should not restrict our definition of life to things that can self-reproduce. It's also true that we should not restrict our definition to things that reproduce badly (e.g. mutation/variation). I can easily imagine living things that could reproduce perfectly—they just wouldn't evolve by any mechanism we currently recognize.

Life is like pornography [I know it when I see it]. In the words of US Supreme Court Justice Potter Stewart,

I shall not today attempt further to define the kinds of material I understand to be embraced within that shorthand description ["hard-core pornography"]; and perhaps I could never succeed in intelligibly doing so. But I know it when I see it, and the motion picture involved in this case is not that.

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Weep for the Poor Persecuted IDiots

 

The Intelligent Design Creationists at Evolution News & Views and Uncommon Descent have been pushing the idea that acceptance of evolution is associated with moral decay and the rise of Adolph Hitler. Recently, an IDiot going by the pseudonym of "kairosfocus" posted a similar attack on his blog: Visually exposing the Anti-Christ spirit of Nazism (and correcting the New Atheist "Hitler was a Christian" smear often used in retort to exposing* the Social Darwinist history of ideas roots of Hitler's thought.

The goal, obviously, is to link the scientific fact of evolution to the evils of social Darwinism and eugenics.

Somebody posted as comment on that blog (or a related blog) saying ...

xxx, the religious wacko who owns and runs this site, blames all the world’s ills, including Hitler and the nazis, on Darwin, atheists, and material evolutionists.

To see the truth about Hitler and the nazis, see these XXXXXXX:

XXXXXX is a LYING, arrogant, bloviating, sanctimonious, ignorant, uneducated, abusive, delusional god zombie.

See this site for a lot more about XXXXX:

The comment has been removed.

Now "kairosfocus" has complained on Uncommon Descent that such "vandalism" is outrageous and misguided [FOR RECORD: What we are dealing with . . . an example of web stalking and vandalism].

Now, this vandalism of a site wholly unrelated to the matters debated at UD (and tied onwards to a hate site that exploits Google’s freedom of comment policies), was evidently in response to my having posted here at UD, matters linked to the well-known history of ideas roots of Hitler’s thought. I therefore suggest that onlookers examine the Weikart lecture and a discussion of a key clip from Mein Kampf that demonstrated the Darwinist-Haeckelian frame of thought, that beyond reasonable doubt strongly shaped Hitler’s thinking, speech and behaviour. (Those needing documentation on Hitler’s actual attitude to and intentions for the Christian Churches, can look at the recently released Nuremberg investigatory documents here. If after seeing these documents and the like, someone still insists on trying to claim Hitler was a Christian etc etc, s/he is delusional and/or willfully deceitful.)

Furthermore, the behavior of this "vandal" is exactly what "kairosfocus" expects.

As they say, a tree is known by its fruits, and draws sustenance from its roots . . .

(In addition, a note on “blaming the world’s ills.” The likes of this hate-driven commenter will not appreciate or accept that a Bible-believing Christian will hold that much of what ails our world traces to our common challenge of being finite, fallible, morally fallen and too often ill-willed. Hence, our common need for recognition of our moral plight, repentance, forgiveness and moral-spiritual transformation through the gospel. Slander-laced strawmen and scapegoats are ever so much more easy to set up and ignite through irresponsible rhetoric that then clouds, polarises and poisons the atmosphere.)

That refusal to be responsible over a moral hazard closely tied to the Darwinist, evolutionary materialist frame of thought, and that refusal to acknowledge well-established historical facts that are inconvenient to the new atheist agenda are tellingly informative.

The pattern of obsessive, self-justifying, nihilistic hate, stalking, slander, Internet vandalism and abuse is even more informative about an unfortunately significant subset of the New Atheist movement and the danger its patent extremism poses. (After this sort of web vandalism, and worse, can any reasonable person doubt why moderation is necessary to maintain a reasonable tone at UD and elsewhere?)

Ironically, the very conscience benumbed self-justifying by smearing scapegoats that this sort of behaviour demonstrates on the small scale, is what — when such attitudes attained state power — led to the utter breakdown of morality on the grand scale that over 100 million ghosts from the past century tell us never to forget.

Can any reasonable person doubt that had a commentator like the above the power to do as he wished and get away with it, he would do me and my family further harm?

It is time for the New Atheist advocates of evolutionary materialism to take a serious look at what they have been enabling by their intemperate writings and attitudes.

Every atheist blogger gets far worse comments from Christians on a regular basis. Most of us get harassing emails every single day and the authors usually identify themselves as devout Christians doing God's work. These same Christians don't hesitate to send threatening messages to our colleagues and family members in an effort to silence us. Some of the Christian kooks are so dangerous that they have been arrested by police and are currently under forcible confinement in a mental health institution.

Don't weep for the IDiots. They need to examine their own beliefs since it's the creationists who are the biggest threat on these blogs. There must be something wrong with Christianity if that's the kind of activity it promotes. It is time for the Christian opponents of science to take a serious look at what they have been enabling by their intemperate writings and attitudes.

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Monday's Molecule #155

 

We're going to talk about the evolution of this molecule in my class tomorrow. It's a good examples for illustrating some basic principles of molecular evolution.

You need to identify the exact molecule, including the species. Here's a hint: ANKSKGIVWN.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

UPDATE: The winner is Dima Klenchin who was the first to identify the molecule as cytochrome c from tuna (Thunnus alalunga). The figure is from the PDB file 3CYT. This PDB file supercedes 1CYT which was reportedly from another species of tuna.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody

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Recent Advances in Intelligent Design Creationism

 

In case you missed it, 2011 was a wonderful year for the IDiots. There were many "scientific" breakthroughs supporting the existence of god an intelligent designer. Access research network provides a list of the top ten "Darwin and Design" news stories for 2011.

I'll just give you the titles. Most of you have already read these very important science papers. The rest of you can access more information at: Top Ten Darwin and Design
Science News Stories for 2011.

1. 50th Peer-Reviewed Pro-ID Scientific Paper Published
2. The Design of the Butterfly Continues to Inspire and Amaze
3. Woodpecker Drumming Inspires Shock-Absorbing System
4. Stylus Aims to Bridge Gap Between Real World and Artificial Evolutionary Simulation
5. Explosive Radiation of Flowering Plants Confirmed
6. Golden Orb-Weaver Fossil Spider Provides New Evidence for Stasis
7. Complexity in the Universe Appears Earlier Than Thought
8. An Identity Crises for Human Ancestors
9. DNA Repair Mechanisms Reveal a Contradiction in Evolutionary Theory
10. The Limits to Self-Organization Identified

The nice thing about this list is that it gives us a very good view of the quality of data supporting Intelligent Design Creationism. This is the best they have.

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The God helmet is used by Michael Persinger in his neuroscience "research." When you put on the helmet it makes you see God. It's just one of many illusions that supposedly reveal the presence of a supernatural being. Of course it has nothing to do with the content of this post.

The Santorum Amendment

 

Rick Santorum is a potential candidate for President of the United States. He is currently seeking the nomination of the Republican party and so far he seems to be a leading candidate in spite of his bizarre views on many issues. The process involves things called state "primaries" which seems to be a way of generating free publicity for the two sanctioned parties.

Back in 2001, Santorum was a Senator from Pennsylvania. He was a leading proponent of Intelligent Design Creationism and he proposed an amendment to a major education bill that was being considered by the United States Senate.¹ The original Santorum Amendment was described by Santorum in a brief speech ...

This is an amendment that is a sense of the Senate. It is a sense of the Senate that deals with the subject of intellectual freedom with respect to the teaching of science in the classroom, in primary and secondary education. It is a sense of the Senate that does not try to dictate curriculum to anybody; quite the contrary, it says there should be freedom to discuss and air good scientific debate within the classroom. In fact, students will do better and will learn more if there is this intellectual freedom to discuss. I will read this sense of the Senate. It is simply two sentences—frankly, two rather innocuous sentences—that hopefully this Senate will embrace: "It is the sense of the Senate that—

(1) good science education should prepare students to distinguish the data or testable theories of science from philosophical or religious claims that are made in the name of science; and
(2) where biological evolution is taught, the curriculum should help students to understand why this subject generates so much continuing controversy, and should prepare the students to be informed participants in public discussions regarding the subject.

It simply says there are disagreements in scientific theories out there that are continually tested.

The original amendment was drafted by Philip Johnson in consultation with other fellows of the Discovery Institute.

This amendment did not make it into law but a similar version was included in something called a "Conference Report" where it is often cited by Intelligent Design Creationists.

The Conferees recognize that a quality science education should prepare students to distinguish the data and testable theories of science from religious or philosophical claims that are made in the name of science. Where topics are taught that may generate controversy (such as biological evolution), the curriculum should help students to understand the full range of scientific views that exist, why such topics may generate controversy, and how scientific discoveries can profoundly affect society.

Taken at face value, these statements seem to provide an excellent opportunity for science teachers to explain how religion distorts science. They would provide legal justification for teachers who want to describe how religious views conflict with science and why scientific facts, such as evolution, generate so much controversy among religious Americans.

But that's not how the amendments are interpreted by most people. Here's Rick Santorum explaining in 2009 what the amendment really meant. It's clear that many Senators, including Ted Kennedy, were duped.

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1. In American legislatures, it's normal that completely irrelevant material is inserted into bills.

Should Undergraduates Study the Primary Scientific Literature?

 
The short answer to the question posed in the title is "yes" but there are many caveats. One of them is that it depends on what level you are teaching. In my opinion, the value of exposing science students to the primary scientific literature (papers) increases as students progress from first year to the year they graduate. Students in their final year of a science program will gain a lot from being exposed correctly to the scientific literature but students in introductory course will hardly benefit at all—and may, in fact, be harmed if it takes time away from learning basic principles and concepts.

It is important to teach critical thinking and it's important to focus education on basic principles and concepts. Most of the basic principles and concepts in a discipline have been developed over several decades. The work that led to those ideas is (usually) in the primary scientific literature but you can't learn the concept by just reading a few key papers. Evolution is a good example but so is our understanding of how cells generate energy from proton gradients, how enzymes work, and how the information in messenger RNA gets translated into proteins.

I find it helpful to remind myself from time to time that the vast majority of the students I teach will never be scientists and many of them aren't really interested in how to do scientific experiments. They will become average citizens in all kinds of careers that have nothing to do with the basic sciences. Our goal is to make them scientifically literate so they will understand why evolution is true, why homeopathy is bunkum, why they should vaccinate their children, and why humans are behind global climate change. I don't think we can achieve that goal by focusing on the primary scientific literature, especially in the early years of undergraduate education.

C.R.E.A.T.E. is a education project funded by the United States National Science Foundation (Grant No. 1021443). It's goal is "transform understanding of science" by using the primary scientific literature as a teaching tool. Here's how they describe their approach ...

The C.R.E.A.T.E. (Consider, Read, Elucidate the hypotheses, Analyze and interpret the data, and Think of the next Experiment) method is a new teaching approach that uses intensive analysis of primary literature to demystify and humanize research science for undergraduates. Our goal is to use the real language of science—the journal article—as an inroad to understanding “who does science, how, and why?” At the same time, we wish to help students (1) experience authentic processes of science, in particular discussion/debate about experimental data and their interpretation (including ‘grey areas’), (2) recognize the creativity and open-ended nature of research, and (3) see the diversity of people who undertake research careers (i.e. not just the genius/geeks of popular culture). As a complement to teaching based on textbooks, which tend to oversimplify the research process, C.R.E.A.T.E. teaching focuses on on authentic published work--peer reviewed journal articles—with students reading either series of papers produced sequentially from individual labs or series of papers from different labs focused on a single line of research.

By reading/analyzing a set of papers published in series from a single lab, students experience the evolution of research projects over a period of years. Using newly-developed C.R.E.A.T.E. pedagogical tools, that encourage multiple approaches to the material (concept mapping, sketching, visualization, transformation of data, creative experimental design) students gain deep understanding of the methods (and biological content/principles) that underlie each individual experiment of the paper. In class, we emphasize scientific thinking--focusing on understanding both why and how each part of the study was done, by examining the hypotheses underlying each aspect of the study, and analyzing/discussing the data represented in each figure and table. Students learn to interpret complex data, draw conclusions, debate interpretations, and re-represent data (e.g. represent tabled data in graphic form) to aid understanding. Content knowledge is reviewed as students consider the principles underlying the techniques used, as well as the overall context of the scientific question being addressed (e.g. a module focused on regeneration would likely include review multiple aspects of cell division, cell differentiation, gene expression and stem cells, drawing on information students learned in other classes and helping them to apply it in a real-world research situation). C.R.E.A.T.E. students thus learn a variety of transferable learning skills that can be applied to complex scientific reading they do in the future. Students design their own proposed followup experiments at several points in the semester, and debate each other’s proposed studies in a classroom exercise modeled on activities of bona fide scientific grant panels. Such discussions reveal the research process to be openended, with multiple branch points or possible “next directions to go;” thus much less linear and predictable than many students expect. Late in the process, students generate a short list of questions for paper authors that are sent as an email survey to each author (not simply the PI). Responses from multiple authors provide unique behind-the-scenes insight into “the people behind the papers,” humanizing the research experience and showing researchers to be complex individuals much like the students themselves.

Here's an example based on Pattern formation during regeneration in planaria.

This is an approach that views experiment as the primary focus of science whereas I tend to see science as a much broader way of knowing. The C.R.E.A.T.E. approach to undergraduate education emphasizes the doing of science rather than the understanding of the results and how they fit into a bigger picture. It probably does a good job of looking at "trees" but not so good a job when it comes to seeing the "forest."

I don't know the correct balance between teaching principles, ideas, and concepts and teaching the experimental approach taken by actual research scientists in their day-to-day activities. There's no question that lab courses are extremely important but I'm quite skeptical about bringing the study of experimental techniques into the lecture courses if it take time away from the conceptual understanding of the discipline.

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[Hat Tip: Sandra Porter at Discovering Biology in a Digital World: Learn how to use scientific articles in education at the C.R.E.A.T.E. June workshop]

Chris Hogue on Complexity and Evolution

 

Chris Hogue is a Canadian biochemist/bioinformatician who works on protein folding (among other things) at the National University of Singapore. He used to be a professor in my department here at the University of Toronto. I miss him, and wish he were still here.

Chris blogs at BioImplement and he has just started a new series of posts on Complexity and Evolution. His goal is to explain how human design can inform us about evolution. The idea is to refute the arguments of Intelligent Design Creationists who treat intelligent design as something mystical that's1 beyond naturalism.

Here's how Chris explains what's coming ...

The thread connecting these examples of human design is that each one is an analogy to biological evolution, from which evolution may be better understood by laypersons. Now by posting new examples like this, I realize that they may all be stolen by the “intelligent design” (ID) creationists to argue against evolution. My view on ID follows that most clearly expressed in the 2005 court judgment from the Pennsylvania Kitzmiller v. Dover case: “The overwhelming evidence at trial established that ID is a religious view, a mere re-labeling of creationism, and not a scientific theory.” Of course a few scientists have written in defense of evolution and against ID nonsense in the classroom, the most strident of whom is Richard Dawkins. I now add my voice in support, as in his final interview with Dawkins, Christopher Hitchens lamented “It’s the shame of your colleagues that they don’t form ranks and say, ‘Listen, we’re going to defend our colleagues from these appalling and obfuscating elements.’”

So into the breach, I add my voice with some new arguments, after this small bit of throat-clearing. I will try to avoid being derivative as I come armed with my own capacity for inquiry, insight, and argument. My examples will show how ID concepts force the gerrymandering of human design history, and surround it with mystical borders to make their claims. The individual steps in human design are small, slow and absolutely require the intellectual imprinting of lessons by trial and error. Students who are led to think falsely about human design, or any complexity as having mystical origins are harmed by the diminishment of their own aspirations of creativity. We all need to understand how small steps and tools lead to human creativity and any object of complexity. I will reveal these small steps and show, where I can, the failures that led to success.

I know Chris and I can assure you that his upcoming posts will be provocative and informative.

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Plant microRNAs in Your Blood?

 

Last month the science magazines and websites were all talking about a paper by Zhang et al. (2012) published in Cell Research. These workers discovered plant micoRNAs in the serum of mice and humans. The microRNAs seem to come from ingested rice. Presumably the micoRNAs are taken up in the intestine and secreted into the blood in small vesicles. The concentration of the major rice miRNAs in serum is about 10 fM or 10×10^-15 moles per liter.¹

The authors have shown that microRNA MI168a binds to the mRNA of low-density lipoprotein receptor adapter protein 1, inhibiting translation. This leads to the idea that ingested plant microRNAs can regulate the expression of human genes. That's the story that generated the most press [What You Eat Affects Your Genes: RNA from Rice Can Survive Digestion and Alter Gene Expression, Food We Eat Might Control Our Genes].

This is one of those findings where the explanation doesn't make a lot of sense but the data seem sound. It seems very unlikely that small plant RNAs could survive the processing and digestion of rice or any other food and even less likely that they would find their way into the bloodstream where they could play a role in regulating mammalian gene expression. I think I'll wait for confirmation.

It's a shame that none of the articles in the popular press expressed any sort of skepticism. That's one of the problems with science journalism. How do you convey the idea that all scientific results are preliminary until they have been confirmed by others?

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1. That concentration is far below the concentration where effective binding can occur but the idea seems to be that the micoRNAs are contained in small vesicles that subsequently fuse with liver cells and deliver the rice microRNA to the cytoplasm where it can inhibit translation of specific mammalian RNAs. It's difficult to see how one could get an effective concentration of plant microRNA in one of these mammalian cells.

Zhang, L., Hou, D., Chen, X., Li, D., Zhu, L., Zhang, Y., Li, J., Bian, Z., Liang, X., Cai, X., Yin, Y., Wang, C., Zhang, T., Zhu, D., Zhang, D., Xu, J., Chen, Q., Ba, Y., Liu, J., Wang, Q., Chen, J., Wang, J., Wang, M., Zhang, Q., Zhang, J., Zen, K., and Zhang, CY. (2012) Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA. Cell Research 22:107–126 [PubMed] [doi:10.1038/cr.2011.158]

An important correction to several of the figures in this paper has also been published.

Zhang et al. (2012) Corrigendum [doi:10.1038/cr.2011.174]

Carnival of Evolution #43

 
This month's Carnival of Evolution (43rd version) is hosted by The EEB & Flow, a blog written by a large group of people interested in evolution and ecology [Carnival of Evolution #43]. The post was written by Marc Cadotte [Cadotte Lab], a professor in the Department of Evolution & Ecology right here at the University of Toronto.

You no longer need to ponder the mysteries of life, travel the globe making observations, or running complex experiments to test hypotheses; everything you want to know about evolution today can be found by reading the monthly installments of the Carnival of Evolution!

The first installment of 2012 (or is this the last of 2011?) offers a great smattering of many different aspects of current evolutionary understanding. These 26 posts cover many of the major areas of research that define current evolutionary biology.

The next Carnival of Evolution (February) needs a host. Contact Bjørn Østman at Carnival of Evolution if you want to volunteer. Meanwhile, you can submit your articles for next month's carnival at Carnival of Evolution.

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And the Winner Is .....

 

I collected the names of all the undergraduates who got the right answer for Monday's Molecules. I put them on slips of paper and had my colleague, Alex Palazzo draw one of them from a small beaker.

Alex still has a blog on Scienceblogs called Transcription and Translation (formerly The Daily Transcript) but he hasn't blogged very much recently. He's too busy doing experiments.

What name did he draw out of the beaker?

The winner of a free autographed textbook is .....

The Cambrian Conundrum: Fossils vs Genes

The earliest fossil examples of most animal classes and phyla appear in the fossil record at about the same time in the Cambrian (about 530 million year as ago (Ma)). This period of apparent rapid divergence is referred to as the "Cambrian Explosion."

It seemed unlikely that this disparity could have evolved in just a few million years so many scientists have been searching for fossil antecedents in the early Cambrian and Ediacaran (635-541 Ma). Many trace fossils have been found in the past few decades, indicating that the fossil animals of the Cambrian were preceded by small wormlike creatures.

The other approach has been sequence analysis. One can construct molecular phylogenies by comparing the sequences of genes in modern extant organisms. This approach has been highly successful over the past fifty years so that we now know a great deal about the relationship of the various animal phyla. The correspondence between the old morphological taxonomy and molecular evolution is the most powerful evidence we have that evolution explains the history of life [see Twin Nested Hierarchies].

The problem with sequence comparisons has always been getting accurate dates using the molecular clock. It is hard to get an accurate date when dealing with events that occurred 500 million years ago because there aren't very many calibration points. An accurate calibration point is a known time when two lineages diverge.

If there really was a rapid divergence in the Cambrian then one would expect the molecular tree to show this. But it never has. The molecular phylogeny shows that chordates diverged from invertebrates at least one hundred million years before their fossils appear in the Cambrian. Similarly other phyla and classes of animals have their origin long before the Cambrian, according to the molecular clock.

A recent paper in Science extends this comparison by calculating more a more accurate molecular phylogeny using seven housekeeping genes from 118 different species (Erwin et al. 2011). The result is shown in Figure 1 of the paper: "The origin and diversification of animals as inferred from the geologic and genetic fossil records." (Click on the figure to embiggen.)

Do the IDiots Understand Biochemistry and Molecular Biology?

 

We've been discussing whether Intelligent Design Creationists understand enough about biochemistry, molecular biology, and evolution to warrant their criticisms of these fields. The answer is clearly "no" as they demonstrate time and time again.

This time it's an anonymous posting on the premier IDC website, Evolution News & Views [Long Non-coding RNA Punches Another Hole in "Junk Genome" Myth]. The anonymous poster links to a recent paper in Genes & Development that shows a function for a particular long non-coding (lnc) RNA. The paper implies that many of these lncRNAs (up to 400) are expressed in mouse erythroid cells.

Regulatory RNA have been known and studied for at least four decades and various lncRNAs have been characterized over the past twenty years. The IDiot at Evolution News & Views seems to think that this is a new discovery proving that there's no junk in our genome. The facts are quite different.

As I pointed out in my review of The Myth of Junk DNA, the amount of the genome devoted to producing lncRNAs is about 0.1% [Junk & Jonathan: Part 6—Chapter 3]. So, not only have we known about regulatory RNAs for many years, we also know that their genes don't account for very much of the genome, I figure it can't be more than 2% even when you include all of the most optimistic estimates of regulatory RNAs [see What's in Your Genome?].

But the ignorance of the IDiots is much more profound than just being incapable of calculating percentages. The latest posting reveals the depth of their ignorance.

These findings have two important implications. First, non-coding regions of the genome were assumed to be leftover evolutionary relics that no longer play a functional role. The assumption was not due to extensive studies of non-coding regions of the genome, but rather to a commitment to what is known as the central dogma of molecular biology: DNA is transcribed into RNA and RNA is translated into amino acids to make proteins. This was considered the primary purpose of DNA. The non-coding regions were assumed to have no function, and were dismissed as the natural consequence of genetic "junk" accumulating over time. This paper is one among an accumulating corpus of papers discussing new and interesting functions of the non-coding regions of the genome. (See The Myth of Junk DNA by Jonathan Wells for a history of "junk" DNA and additional references describing the function of so-called "junk" DNA. See here for a discussion on the regulatory role of introns.)

There was never a time in the past fifty years when knowledgeable biochemists and molecular biologists thought that all non-coding DNA was nonfunctional junk. This was never an assumption of the Central Dogma of Molecular Biology which states that "... once (sequential) information has passed into protein it cannot get out again" [Basic Concepts: The Central Dogma of Molecular Biology]. There are many scientists who have misconceptions about the Central Dogma [The Central Dogma Strawman] but the IDiots go one step farther by misunderstanding the misconception!

We've known about functions in non-coding DNA since the early 1960s as anyone who has ever glanced at a textbook would know. It's hard to tell whether the IDiots are just butt-ignorant of basic science or whether they are lying. This is an especially tricky problem when the silly strawman argument is popularized by Jonathan Wells because he's supposed to know the science [Junk & Jonathan: Part 1—Getting the History Correct] [Junk & Jonathan: Part 2— What Did Biologists Really Say About Junk DNA?].

We know that most of our genome is junk because we know a great deal about genomes, genes, biochemistry, molecular biology, and evolution. We know which parts are likely to be functional and which parts are likely to be broken genes and other kinds of junk. We know this because we understand the subject, not because we are covering up our ignorance.

The IDiots are ignorant of the science and they assume that everyone else is as well. That's a very bad assumption.

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Center for Inquiry Canada: New Associate Members

 
The Board of Directors voted on accepting new Associate Members at its December 11th meeting. I have just received a letter from the Board signed by the new (?) Chair, Richard Thain.

Dear Professor Moran,

On December 11, 2011 one of the many important items on the agenda for the Board od Directors meeting was discussion of the applications for Associate Membership.

The goal is to have a diverse group of Associate Members which reflects our membership geographically. In order to achieve this, the Board recognizes that we must update our website and post the By-Laws which explain the governance of CFI Canada. We hope to attract more applications which will then be reviewed before the next CFI Canada AGM in March 2012.

We felt it was important to approve some of the applications at the December 11th board meeting, so we reviewed and accepted the following five people:

Iain Martel, Seanna Watson, Brian Eelhart, Craig Irving and Marlowe Filippov.

The other applications were put under review and will be considered with the next wave of applicants at a future board meeting.

The Board of Directors realizes you have made and are continuing to make significant contributions to our success. We would like to sincerely thank you for your continued support and committment to helping CFI build a better Canada through reason.

Richard Thain DDS
Chair, Board of Directors
CFI Canada

My application was rejected!

I wish I knew why the Board didn't accept my application but did accept some others. Iain Martel is the Chair of CASS and Seanna Watson is the Director of the Ottawa branch of CFI so I assume that the people filling these positions are a sort of ex officio Associate Members. That makes a lot of sense especially for Iain and Seanne who have devoted so much time and effort to CFI.

Bryan Eelhart was the Financial Agent for the Green Party in the riding of Trinity-Spadina (Toronto) during the recent Ontario election. He's a member of the Board of Directors at Conscience Canada and he works for Science for Peace. Bryan has extensive expertise in website design and implementation.

Craig Irving is a freelance videographer from Toronto. He serves on the Multimedia Committee at Centre for Inquiry Canada.

Marlowe Filippov lives in Ottawa where she volunteers at the Centre for Inquiry. She's also an expert in websites. She's been helping out with membership problems and advising the National Director on other issues.

It appears that three two of the new Associate Members were chosen for their ability to help out with updating the CFI website.

There are currently three Associate Members who are CFI Advisory Fellows; Jeff Rosenthal from Toronto, Chris diCarlo from Guelph, and Ethan Clow from Vancouver. It's possible that the Board of Directors felt that only three CFI Canada Advisory Fellows should also be Associate Members, or maybe they felt that having two from the Toronto area was too much and that's why my application was rejected.

I'll try and find out more about the qualifications required for Associate Membership. It's clear that length of membership in CFI is not important since there are Associate Members who only joined CFI two years ago. I think that active volunteering on administrative tasks is an important criterion so if you are currently helping out in this area you will probably have a good chance of being appointed.

I'm a little unclear about the criterion of reflecting membership geographically. About half of all CFI Canada members are from the Toronto area but I don't think this means that half of the Associate Members will be from Toronto. I think it means that you're more likely to be chosen as an Associate Member if you are from one of the other centres that isn't already represented.

I'm not sure what the role of a CFI Canada Advisory Fellows is supposed to be. If we can't be Associate Members then who are we supposed to advise? :-)

Post a comment if your application was also rejected. That way we might be able to figure out what the Board of Directors is thinking when it comes to appointing new Associate Members. I'll let the Board know about this posting so they can comment, or at least see your comments.

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A Torley Defense of Irreducible Complexity

Vincent Joseph Torley (vjtorley) has a Ph.D. in Philosophy (2007) from the University of Melbourne (Australia). He currently teaches English in Japan.

Torley hangs out at Uncommon Descent where he tries to defend Intelligent Design Creationism. He didn't like my recent posting on Irreducible Complexity [Barry Arrington Explains Irreducible Complexity] because I accused Barry Arrington of not understanding evolution. You might recall that Arrington began his defense of irreducible complexity by saying, "(1) By definition, evolution can work only in a stepwise fashion wherein each successive step is “selected for” because it has conferred a selective advantage on the organism."

This is not how evolution is defined and it's a particularly bad way to begin because the scientific understanding of many irreducibly complex systems involves the fixation of neutral or even detrimental alleles. Competency in evolution also requires an understanding of redundancy, contingency, and sloppiness.

Vincent Joseph Torley asks, "Will this do, Professor Moran?" He starts with ....

Let me state up-front that I am a philosopher, not a scientist. However, I believe in arguing rigorously, so I have attempted to state the argument from irreducible complexity in a rigorous fashion. I’d appreciate hearing from Professor Moran thinks of this argument, as a biologist.