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.

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.

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.

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.)

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

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.

1. Introns are mostly junk. I think PZ exaggerated a bit when he dismissed all introns as junk. My position is that we should treat introns as functional elements of a gene even though many (but not all) of them could probably be deleted without affecting the survival of the species. Each intron has about 50-80 bp of essential information that's required for proper splicing [Junk in Your Genome: Protein-Encoding Genes]. The rest of the intron, which can be thousand of base pairs in length, is mostly junk [Junk in Your Genome: Intron Size and Distribution]. Some introns contain essential gene regulatory regions and some contain essential genes. That does not mean that all intron sequences are functional.

2. Telomeres are not junk. I don't think telomeres are junk [Telomeres]. They are absolutely required for proper DNA replication. PZ Myers agrees that telomeres (and centromeres) are functional DNA (28 minutes into the talk). Jonathan McLatchie claims that PZ describes telomeres as junk DNA, "Myers departs from the facts, however, when he asserts that these telomeric repetitive elements are non-functional." McLatchie is not telling the truth.
3. Defective Transposons are Junk. PZ Myers talks about transposons as mobile genetic elements and states that transposons make up more than half of our genome. That's all junk according to PZ Myers. My position is that the small number of active transposons are functional selfish genes and the real junk is the defective transposon sequences that make up most of the genome [Transposon Insertions in the Human Genome]. Thus, I differ a bit from PZ's position. Jonathan McLatchie, like Jonathan Wells, argues that because the occasional defective transposon in the odd species has acquired a function, this means that most of the defective transposon sequences (~50% of the genome) are functional. This is nonsense.

Nobody else is doing what the Discovery Institute has been able to do, and that is really put an entire scientific establishment on the defensive, forced for the first time to respond to some very significant criticism...

On Sunday, December 11, the Associate Members of CFI Canada met in Toronto. This meeting was followed shortly thereafter by a meeting of the board of directors. We, the board, believe it is important to provide you with information about these meetings and the actions and decisions that took place at these meetings.

The meeting of Associate Members was scheduled pursuant to the by-laws of our organization, that is, it was scheduled after the requisite number of Associate Members requested the meeting. The request for the meeting indicated its purpose was to consider the separation of Justin Trottier from the position of National Executive Director (NED), so that topic was discussed. Justin Trottier, who was present at the meeting, was provided a summary of the concerns of some of the directors and he was provided an opportunity to address those concerns. Some Associate Members also expressed their views, as did some of the Regional Executive Directors who audited the meeting.

We believe there was a frank and candid discussion of Justin Trottier’s tenure and the circumstances that led to his separation. We also believe this frank, candid exchange of views was of benefit to the organization.

Shortly after the Associate Members meeting, the board met. One of the issues considered was increasing the number of Associate Members. Among the decisions of the board on this issue were the following:

• The board unanimously agreed to invite additional applications to the position of Associate Member, to ensure broader representation of the supporters of CFI Canada in this important class of membership;
• Application forms can be obtained from the Interim NED, Michael Payton (mpayton@cficanada.ca), or from Kevin Smith, Secretary for the board;
• Because the primary duty of the Associate Members is to elect directors at the organization’s annual meeting, applications will be reviewed carefully, and emphasis will be placed on the applicant’s prior work for and familiarity with the organization, as well as commitment to its mission;
• The board concluded, consistent with the by-laws, that Associate Members should be a subset of the general membership and that the number of Associate Members should be kept at a manageable level;
• The board resolved to act on applications in a timely manner so that applicants would be informed of their status prior to the March 11 annual meeting;
• The board considered and acted on some of the applications it received prior to the December 11 meeting, and accepted applicants will be notified via email.

The board heard a report on the organization’s finances and the status of the organization from Interim NED Michael Payton. Although the organization has no cash crisis, and has sufficient assets to maintain operations in 2012, it was apparent that the organization needs to make efforts to increase donor support, and the board directed Mr. Payton to undertake fundraising. The Interim NED indicated he needed assistance in his new position to deal with the many tasks which require immediate attention.The board expressed appreciation for Mr. Payton’s willingness to step in quickly and assume the Interim NED position given the sudden departure of the prior NED. The board authorized Mr. Payton to seek volunteer assistance and stated it would consider a request to authorize
hiring of additional staff.

The board decided the branding initiative would continue, but that it would be put on hold given the current status of the organization. The organization’s first priorities are to ensure stability and reliable management, raise money, and begin to offer regular programming and services again as soon as possible.

After appropriate motions, the board resolved the following:

• No final decision would be made on Justin Trottier’s possible reemployment in any position until the March 11 board meeting. In reaching this decision, the board carefully considered the views that had been offered concerning Mr. Trottier, both pro and con, as well as his record as NED. We also took into account the fact that we agreed to retain our current NED untill March at which time he will
  voluntarily step down.
• The board would look favorably upon Mr. Trottier’s volunteering of his services to CFI Canada during the period prior to the March 11 board meeting.
  Lorne Trottier took no part in the voting on these motions. The motions carried 3-0, with Tom Flynn absent and Kevin Smith abstaining.

After the board meeting, the board was informed that Justin Trottier would volunteer to assist the organization. CFI Canada welcomes his willingness to volunteer, as it welcomes the willingness of all its volunteers to donate their valuable time and energy to furthering our mission.

One other item the board discussed at length was the perception that there is a lack of transparency and openness in board deliberations. To that end the board will be doing some renovations to the web site which will include, among other things, the posting of our by laws. We will also make available, the application to become an Associate Member along with the guidelines for applying. We will also have a dedicated email so CFI supporters can directly contact the board, the email directors@cficanada.ca
will be up by starting Thursday Dec 15th.

The board is committed to using its best efforts to ensuring not only the survival, but the success of CFI Canada and its important mission. We are well aware that many of the decisions we make are bound to be controversial. We cannot please everybody. At the end of the day we have to rely on our judgment. Our service as directors is not perpetual. Associate Members will be able to reelect or remove us at the March 11 meeting. In the meantime, we pledge to you that we will act in good faith, motivated by what we think is best for the organization and its missio

Thank you for your support.

No ID theorist has ever argued that evolution is impossible because complex biochemical systems cannot self assemble “all in one go.” This is an absurd caricature of the argument from irreducible complexity (IC).

The basic logic of IC goes like this: (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. (2) an irreducibly complex system is a system which if one part is removed all function ceases. (3) by definition, therefore, an irreducibly complex system cannot be produced in a stepwise fashion. (4) therefore evolution is not capable of producing an irreducibly complex system.

Starting with this logic the ID proponent argues that certain systems are irreducibly complex and therefore could not have been produced by evolution. The bacterial flagellum and the blood clotting cascade are classic examples of such systems.

This is the type of condescending rhetoric that is so prevalent in anti-ID writings. Does Shallit really think that we haven't heard of processes such as genetic drift and endosymbiosis?

Atheists deny that God exists. Yet for an atheist to make our ranking of the 50 top atheists in the world—given in ascending order—it is not enough merely to deny that God exists. More is required.

Certainty. To make our list, someone has to be very sure of him- or herself. No mere agnostics will do. To make the cut, one has to do more than merely question God’s existence or even deny that knowledge of God’s existence is possible.

Celebrity is another requirement. To make our list, the atheist must have a public identification with atheism and must have made some public impact by challenging religion and/or promoting atheism, either in print or on the Internet. In other words, our ranking is a list of people who are well known because they are atheists, among other things—as opposed to people who are mainly famous for some other reason (like Jodie Foster or Bruce Willis). In a few cases, a person has made the list mainly on the basis of his or her attack on free will and morality—the foundation of the traditional religious view of human beings—so long as the person has also publicly identified as an atheist.

Don’t panic — welcome to the forty-second Carnival of Evolution! Please bear with me and pretend it’s still Dec 1st — I had just recently emerged from a wormhole in time, caused by being in a protistologist’s heaven: Dalhousie University in Halifax, with about 30-40 dedicated protist geeks milling about. It was distracting and a pleasant contrast to being the only one in an entire state…

But now I’m back in a very evolution-ey place, just in time for a collection of equally evolution-ey posts from all four corners of the internet! (tubes have corners, right? No? Oh…)

Apologies if I missed any; there are a lot of submissions this month… will correct noted omissions and errors!

CASS continues to meet and there are many projects under way. One of the co-directors, Michael Kruse, resigned because he wasn't happy with the direction that CFI was headed. The other co-director, Iain Martel is carrying on.

Right now this branch doesn't exist as far as I can tell. There's no leader and no volunteers are working.

The acting National Executive Director is Michael Payton. He is struggling to get a grip on the organization after the abrupt departure of Derek Pert a few weeks ago. (Derek was forced to resign when the Board of Directors failed to support him.) The former National Executive Director, Justin Trottier, was fired last September.)

Michael could use a lot of help but there's no room for anyone else in the new office. Don't expect the website to be updated in the near future. Don't expect any memberships to be renewed—and certainly don't expect to be notified if your expires. Don't even expect any email messages from the head office.

Michael is leaving for Singapore in a few months and there's nobody who looks like they could step into his job.

Three members of the Board of Directors resigned two weeks ago (Carol Parlow, Ian McCuaig, and Michael Gardnier). The remaining Canadian members are: Kevin Smith, Lorne Trottier, Pat O'Brian, and Richard Thain. The representatives from CFI Transnational are Ron Lindsay and Tom Flynn.

The Associate Members elect the Board of Directors. In addition to the current directors and the three who resigned there are six Associate Members: Chris DiCarlo, Jeffrey Rosenthal, Zak Fiddes, Ethan Clow, Bisi Bashorun, and Barry Karr. (Barry Karr is from CFI Transnational.)

As far as I know, only three of these are active: Chris DiCarlo, Jeffrey Rosenthal, and Zak Fiddes.

There's going to be a meeting this Sunday. It was called by a group of Associate Members. The first part of the meeting is between the Board of Directors and the three active Associate Members. The second part of the meeting is a Board meeting.

The main item on the agenda is whether the firing of Justin Trottier was fair. I believe Justin will be at the meeting. There's talk of a plan to re-hire him in some capacity. It's clear that some members of the Board are sympathetic and it's clear that some are adamantly opposed. It doesn't look like the dissention within the Board has gone away after three resignations.

Some of us tried to make the Sunday meeting an open meeting for all members of CFI but that plan met with firm resistance from the Directors.

There's general agreement that we need new Associate Members. Several people have sent in applications. New members have to be approved by the Board of Directors. They will discuss this at the Sunday meeting.

The rebranding exercise is on hold, and so is everything else.

I'm going to let ENV readers in on a little secret: When many of us in the intelligent design (ID) movement read the arguments coming from our critics, we're surprised at their low quality and style. We don't rejoice at this -- we'd much rather see a robust, civil, and fruitful scientific debate over the relevant questions. But the incivility, basic inaccuracy, and unserious tone characteristic of so many criticisms of ID all make you wonder: If the critics had stronger rebuttals to offer, wouldn't we be hearing them?

...

There are so many examples of incivility among ID-critics that it's hard to know where to start. And I'm not just talking about the usual Internet suspects, like PZ Myers, Jerry Coyne, or Larry Moran.

I threw down the gauntlet to many of my Darwinian opponents by telling her that if Darwinism is indeed a purposeless, non-teleological process, as many evolutionists and biology textbooks proclaim, and if morality is the product of these mindless evolutionary processes, as Darwin and many other prominent Darwinists maintain, then "I don't think [they] have any grounds to criticize Hitler."

According to Flam, these are "fighting words." However, I have spoken with intelligent Darwinists who admit point-blank that they do not have any grounds to condemn Hitler, so I am not just making this up. Many evolutionists believe that since evolution explains the origin of morality -- as Darwin himself argued -- then there is no objective morality. The famous evolutionary biologist and founder of sociobiology, E. O. Wilson, and the prominent philosopher of science Michael Ruse co-authored an article on evolutionary ethics in which they asserted, "Ethics as we understand it is an illusion fobbed off on us by our genes to get us to co-operate."

At the Discovery Institute we often offer an inter-faith Prayer of Thanksgiving to the Almighty for the likes of P.Z. Myers, Larry Moran, Barbara Forrest, Rob Pennock and Jeffrey Shallit.

Le Canard Noir / Andy Lewis,

I represent the Burzynski Clinic, Burzynski Research Institute, and Dr. Stanislaw Burzynski. It has been brought to our attention that you have content on your websites http://www.quackometer.net/blog/2011/11/the-false-hope-of-the-burzynski-clinic.html that is in violation of multiple laws.

Please allow this correspondence to serve as notice to you that you published libelous and defamatory information. This correspondence constitutes a demand that you immediately cease and desist in your actions defaming and libeling my clients.

Please be advised that my clients consider the content of your posting to be legally actionable under numerous legal causes of action, including but not limited to: defamation Libel, defamation per se, and tortious interference with business contracts and business relationships. The information you assert in your article is factually incorrect, and posted with either actual knowledge, or reckless disregard for its falsity.

The various terms you use in your article connote dishonesty, untrustworthiness, illegality, and fraud. You, maliciously with the intent to harm my clients and to destroy his business, state information which is wholly without support, and which damages my clients’ reputations in the community. The purpose of your posting is to create in the public the belief that my clients are disreputable, are engaged in on-going criminal activity, and must be avoided by the public.

You have a right to freedom of speech, and you have a right to voice your opinion, but you do not have the right to post libelous statements regardless if you think its your opinion or not. You are highly aware of defamation laws. You actually wrote an article about defamation on your site. In addition, I have information linking you to a network of individuals that disseminate false information. So the courts will apparently see the context of your article, and your act as Malicious. You have multiple third parties that viewed and commented on your article, which clearly makes this matter defamation libel. Once I obtain a subpoena for your personal information, I will not settle this case with you. Shut the article down IMMEDIATELY.

GOVERN YOURSELF ACCORDINGLY.

Regards,

Marc Stephens
Burzynski Clinic
9432 Katy Freeway
Houston, Texas 77055

If you had no history of lying, and if you were not apart of a fraud network I would take the time to explain your article word for word, but you already know what defamation is. I’ve already recorded all of your articles from previous years as well as legal notice sent by other attorneys for different matters. As I mentioned, I am not playing games with you. You have a history of being stubborn which will play right into my hands. Be smart and considerate for your family and new child, and shut the article down..Immediately. FINAL WARNING.

Regards,

Marc Stephens

• Mike's Weekly Skeptic Rant: Burzynski Clinic - Medical Quacks and Legal Blowhards
• Pharyngula: Burzynski Clinic: the domain of scoundrels and quacks
• The Quackometer: The Burzynski Clinic Threatens 17 Year Old Blogger
• Respectful Insolence: Marc Stephens issues more threats on behalf of the Burzynski Clinic
• Science-Based Medicine: Stanislaw Burzynski: Bad medicine, a bad movie, and bad P.R.
• Skeptic North: Burzynski Clinic? Meet the Streisand Effect

In order for extraterrestrial organic matter to have fueled the origin of life, a lot of meteorites carrying organic matter had to arrive on the primitive Earth. The problem of amino acid concentrations and stabiltity were discussed in a classic paper by Jeffrey Bada published in 1991.

Some of his calculations are worth remembering.

The current flux of extraterrestrial organic material is about 3 × 10⁸ grams per year from cosmic dust and micrometeorites. About 1% of this is amino acids and most of them are not the ones found in living organisms. This should give rise over time to a concentration in the oceans of about 0.1 nM (10^-10 M). That's not sufficient for life to have originated.

The flux in the past was almost certainly much greater and lots of organic material might have been delivered by large meteorites; however, it's unlikely that amino concentrations in the oceans could ever have been more than 10-100 pM for all amino acids combined.

Most amino acids will spontaneously degrade over time. There's a window of opportunity that only lasts about 10 million years because in that time all the water in the oceans will pass through hydrothermal vents and the high temperature will destroy most chemicals—including amino acids.

First, Larry points out that arguments about the existence of God require one to take a position on fairies. One can only be agnostic about gods to the extent one is agnostic about fairies. My previous argument that this is comparing unlikes has, in one fell swoop, been demolished! Of course, there must be other reasons for thinking that we can rule fairies out of contention (let us call them faeries to avoid confusion) which do exist but are undetectable. It cannot be the principle that “if it is unscientific it is irrational” for that would be the positivist presumption and that would be unscientific. I know I am wrong about positivism here, because Dan Hicks pointed out that some positivists weren’t positivists about everything. So positivism is never self-defeating, even when the positivist presumption is applied by some to everything.

Larry must have other reasons for showing that faeries do not exist – other than being uninterested in what some people claim; this, as Larry must appreciate, is not about what I the reasoner think is true, but about what others who make these claims must be called. I look forward to him enlightening me on this.

atheist: a person who denies or disbelieves the existence of a supreme being or beings [dictionary.com]

atheist: a person who does not believe in the existence of God or gods [Oxford Dictionaries]

Effective population size is "the number of breeding individuals in an idealized population that would show the same amount of dispersion of allele frequencies under random genetic drift or the same amount of inbreeding as the population under consideration."

N). Sometimes it's a lot less. In most vertebrates, for example, the long-term effective population size is calculated to be about 10,000.

Why is this important? It's important because evolution is important for understanding biology and in order to understand evolution you need to understand population genetics. One of the important lessons from population genetics is that the relative important importance of natural selection and random genetic drift is dependent on effective population size. This is a major theme in Michael Lynch's book The Origins of Genome Architecture.

He argues that the effective population size of most large multicellular animals (e.g. Homo sapiens) was small enough to render natural selection impotent for most alleles that might have been somewhat beneficial in larger populations. This led to loss of such beneficial alleles by random genetic drift and to frequent fixation of mildly deleterious alleles by drift. Thus, even if the accumulation of large amounts of junk DNA, for example, was slightly deleterious, it cannot be eliminated by natural selection when the effective population size is small.

Furthermore, many alleles with small beneficial effects cannot possibly become fixed in such a population so it's silly to construct a model that relies on fixation of alleles with a small advantage. This leads to his theory of the evolution of genome complexity by nonadaptive processes. According to Lynch, the default explanation is random genetic drift and because this accounts for much of genome architecture, there's no reason to invoke natural selection to explain what we observe.

Lynch devotes an entire chapter (Chapter 4) to Why Population Size matters. I'm hoping to get more people interested in this subject by giving them a simple example of the difference between actual population size (N) effective population size (N_e).

This isn't only important in genome evolution. As most of you know, the effective population size is an important consideration in recent human evolution [From genes to numbers: effective population sizes in human evolution] and many other disciplines.

---

1. The reason we focus on nobility isn't because they are more important, genealogically, than the 8,000 other soldiers at the battle. It's because we don't have any records of those other potential ancestors.

2. This doesn't mean that all of the alleles in the other 20 individuals were lost because many of them could have been passed down from siblings, aunts, uncles etc.

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