Tuesday, July 13, 2010

Copenhagen Declaration on Religion in Public Life

The recent Gods and Politics conference in Copenhagen adopted the following Declaration on Religion in Public Life. The conference was the first European event of Atheist Alliance International, and was co-hosted by AAI and the Danish Atheist Society.
We, at the World Atheist Conference: "Gods and Politics", held in Copenhagen from 18 to 20 June 2010, hereby declare as follows:

- We recognize the unlimited right to freedom of conscience, religion and belief, and that freedom to practice one's religion should be limited only by the need to respect the rights of others.

- We submit that public policy should be informed by evidence and reason, not by dogma.

- We assert the need for a society based on democracy, human rights and the rule of law. History has shown that the most successful societies are the most secular.

- We assert that the only equitable system of government in a democratic society is based on secularism: state neutrality in matters of religion or belief, favoring none and discriminating against none.

- We assert that private conduct, which respects the rights of others should not be the subject of legal sanction or government concern.

- We affirm the right of believers and non-believers alike to participate in public life and their right to equality of treatment in the democratic process.

- We affirm the right to freedom of expression for all, subject to limitations only as prescribed in international law - laws which all governments should respect and enforce. We reject all blasphemy laws and restrictions on the right to criticize religion or nonreligious life stances.

- We assert the principle of one law for all, with no special treatment for minority communities, and no jurisdiction for religious courts for the settlement of civil matters or family disputes.

- We reject all discrimination in employment (other than for religious leaders) and the provision of social services on the grounds of race, religion or belief, gender, class, caste or sexual orientation.

- We reject any special consideration for religion in politics and public life, and oppose charitable, tax-free status and state grants for the promotion of any religion as inimical to the interests of non-believers and those of other faiths. We oppose state funding for faith schools.

- We support the right to secular education, and assert the need for education in critical thinking and the distinction between faith and reason as a guide to knowledge, and in the diversity of religious beliefs. We support the spirit of free inquiry and the teaching of science free from religious interference, and are opposed to indoctrination, religious or otherwise.
Adopted by the conference, Copenhagen, 20 June 2010.
Please circulate this as widely as you can among people and groups who advocate a secular society.

Friday, April 23, 2010

Selection, Neutrality, and the Appearance of Design

Jerry Coyne has just released his review of two books: The Greatest Show on Earth and What Darwin Got Wrong over at The Nation. Now, a lot of reviews all over the blogosphere have already ripped What Darwin Got Wrong to shreds, and I won't do so again here because I think they have touched all of the bases pretty well. That said, I do have a problem with a phrase that Jerry Coyne made in his blog post (here) linking to his review of the two books. And that is this:

I decided to use the review as a chance to lay out the reasons why biologists accept selection as the only plausible process that produces the appearance of “design” in organisms. (Note to Larry Moran: of course it’s not the only process that causes evolution!)

Now, while Dr. Coyne is acknowledging that other evolutionary processes exist, namely random genetic drift a point often belaboured by Dr. Moran, I take issue with the recurring notion that Selection is the only mechanism capable of producing features that look designed, and I just don't think that is true.

A paper published in 1999 by Arlin  Stoltzfus (who is doing an excellent series of guest posts over at The Sandwalk)called On the Possibility of Constructive Neutral Evolution (here) addresses this. I have mostly been exposed to this topic through my time as a graduate student. Because we study molecular evolution, I think that the idea of Neutral Evolution is much more firmly planted in our minds than it is for many evolutionary biologists, and I have certainly absorbed that paradigm. Neutrality, for me, is the proper default null hypothesis for evolutionary features. Adaptationist explanations require evidence of selection, selection should not be assumed by default.

So what is Constructive Neutral Evolution? Well my primary exposure to this concept, at leats layed out as a package deal, has been talks by Ford Doolittle. For an in depth opinion/review of a recent talk on the subject that Ford gave by an undergraduate student see a post by PsiWavefunction here. In brief Constructive Neutral Evolution lays out how complex features can arise without the complexity of the mechanism being selected for. In the realm of molecular biology there are lots of transient and accidental interactions between molecules.

In brief, Constructive Neutral Evolution and the building of complexity is a ratchet mechanisms. These transient (and unselected for) interactions provide the opportunity for the stabilization of mutations in one or the other binding partner that would otherwise have been deleterious. Under small population sizes these "deleterious" mutations can become fixed and the transient accidental interaction is now required. We have moved from a one component to a two component system, with the two component system now unable to go back. It has moved to be more complex, without positive selection being what drove this increase in complexity, and appearance of design.

I am sure we will see more on this subject over at The Sandwalk. More in depth reading can be done at PsiWavefunction's blog linked above, or even better if you have access read the original paper that I also linked to.

Edit: Some Additional Links:

Rosie Redfield commented on a talk given by Ford Doolittle on the subject here as well that is quite informative and PsiWavefunction has notes posted from the same talk here

Thursday, November 13, 2008

Bad press releases and "revolutions of science

This is a repost of something I just recently posted elsewhere in relation to this crappy article about this press release about this paper. I will stress at the beginning, although I talk about this further down, that I think the paper is pretty good. I don't think it is "earth shattering" or revolutionary, and I detest the way that press releases, even from Universities, tend to use this sort of, frankly inflammatory, language when talking about scientific research. Evolution of evolutionary rates, omptimization processes, etc have all been talked about for awhile in molecular evolution and this paper doesn't completely change how we think about evolution at all. This post also goes into some other things which are tengentially related to talk about this issue before getting into my discussion of the press release and paper itself.

Well hopefully my little diatribe here will help clear some things up. Because it is important to remember that Evolution != Random Mutation + Natural Selection. And it hasn't for quite some time, at least since the synthesis and definitely since the formulation of Neutral Theory. Unfortunately even many non-Creationists and evolution supporters put forward that weakened, watered down, over simplified version as being "evolution" when it isn't. Hell in some surveys even publications like Nature have done it, and it's wrong. People who work in evolution, particularly molecular evolution, have railed against that for a long time. So, with my rant out of the way...

Darwin's original three postulates upon which the theory of evolution was built are simply the following:

* The ability of a population to expand is infinite, while the resources available to sustain said population are finite. This dynamic causes a struggle for existence among individuals as they compete for resources.
* Organisms vary in their physical qualities; these variations allow some members to reproduce more successfully than others.
* These variations are inherited by offspring from their parents.

Note that there is no talk about the source of variation here, and that was one of the major flaws in Darwin's work as perceived by others, he had no mechanistic explanation with how such variation came to be introduced into populations, because he was unaware of Mendel's work. It wasn't until the 1900's, after the re-discovery of Mendel's work that we started talking about genes and mutations, etc. And these three postulates, simplified as they are, still hold true.

For those not aware, there are a lot of different types of mutations including the common point-mutation that everyboyd knows and loves. But there are also larger scale mutations such as insertions and deletions, inversions, chromosomal/genomic amplifications (including the subset of gene duplications), gene fusion events, chromosomal rearrangements, etc. Setting that groundwork is very important because the diversity of what we are talking about in terms of mutations is pretty broad and capable of some pretty amazing things. Gene duplication followed by divergence and neo-functionalization is something very important in terms of the evolution of new protein functions and surprise surprise adds new information to the genome. Gene fusion events happen and so you can end up with two formerly interacting genes now being one gene, inversions can re-arrange the order of protein domains while leaving the protein functional, etc. There is a lot going on.

The Neutral Theory of Molecular Evolution was introduced by Kimura in the late 1960's. Unfortunately early on some people took it as being an argument against selection and evolution although it never was, Kimura was carefult o stress that it was complimentary. There are still debates about the relative importance of selection versus drift but neutral evolution today is well accepted, particularly among molecular evolutionary biologists, and neutrality typically is our null hypothesis in terms of selection. Neutral theory illustrated the fact that mutations are not just beneficial or deleterious, there are also two other classes of mutations: neutral (no selective effect) and nearly neutral (weak selective differences either positive or negative). Selection and Genetic Drift are oposing forces in evolution. Drift is a purely random process introduced by stochastic sampling biases in sexually reproducing organisms. It can be quite powerful in terms of resulting in the fixation or loss of allelic variants in a population in the presence of even weak selection but most particularly when selection is non-existent. This can be a very powerful force in terms of driving speciation. In fact in Peripatric Speciation drift is thought to be a very important factor due to founder effects and population bottlenecks. For anyone interested in genetic drift, speciation, mutation, and how allele frequencies change in populations you may want to look into the field of Population Genetics, a sub-discipline (essentially) within evolutionary biology that studies population level effects on allelic frequencies.

Now, back to the paper at hand. The Princeton press release is better than the linked article by far, although I still take issue, as usual, with lots of the language used in these sorts of press releases. "Until now evidence of this was lacking", etc. They all irritate me. I think the work done by this lab was important, but it isn;t revolutionary. It is another really well laid out example of some of sorts of things that have been talked about and studied in molecular evolution for awhile. here is the link to the actual research article which you should be able to view if you have academic access to the journal. This paper is interesting and is good experimental evidence, and a reuslting analytical framework for what they call control optimization, in this case of redox potentials in the electron transport chain (Cytochrome b in particular). It isn't, in my opinion, revolutionary. Press releases are frequently really, really bad and tend to overhype findings and put them in the context of "changing everything we know" which simply isn't true. That said at a glance this seems like pretty good and interesting work and I'm going to read it in much more detail when I can, in particular because there may be something there that helps me in my own work, maybe. We'll see. So I just want to talk about a few other things in this post as well.

Compensatory mutations have been known for a long time. If you have a coding sequence for a protein and let's say a mutation in site i of that protein which results in the change from a relatively large amino acid, such as tryptophan, to a small one like alanine. Now site i was in interaction with site j, which had a relatively small amino acid at that position. Due to the mutation the interaction between these two amino acids is weaker or perhaps non-existent which, for the sake of argument we will assume has an effect on the function which makes the protein less efficient but doesn't result in the death of the organism or anything very drastic. Now, over evolutionary time any mutation nat site j which restored or strengthened that interaction will be beneficial because it improves function, this may even happen relatively quickly because the selective advantage of the compensatory mutation is quite high and so it may become fixed in the population quite quickly. Those are compensatory mutations and we've known and talked about and studied them for quite some time in molecular evolution.

Things like co-evolution and co-evolutionary rates have also been known for awhile, with many studies, such as this one being some examples of that sort of thing. The take home message is that functionally related proteins and, more importantly, functionally interacting proteins, tend to have correlated evolutionary rates. It is a simple extension of both neutral theory and natural selection which is actually somewhat intuitively obvious.

For those interested I thought I would also provide a link about the evolution from RNA to DNA. Why? Well because it goes along with my next topic which is the molecular repair machinery. So DNA repair effects things like mutation rates, because it fixes lots of mutations before they can be passed on to the next generation. But as you are reading about them keep in mind a few things.

1) Repair mechanicms are not perfect, like all molecular mechanisms they are "leaky"

2) Depending on the type of damage being repaired they can actually introduce changes themselves. For instance if there is a base mismatch between the two strands of DNA the repair mechanism has only a 50/50 chance of repairing it correctly, it doesn;t KNOW what the coding strand is, it just fixes the mismatch pretty much at random. So it may repair the mismatch correctly or, in the repair process, actually introduce a mutation in the coding sequence.

3) The DNA repair machinery is coded for on the DNA itself, meaning that it is also subject to mutation and selection. That means that the rate and accuracy of DNA repair mechanisms play a role in determining the rate of evolution itself. Leaky or error-prone repair mechanisms tend to result in a higher rate of mutation and thise a higher rate of evolution, stricter and more accurate repair mechanisms result in the opposite. It's a fine line and trade-off and there is ample evidence of selection on DNA repair mechanisms, particularly among mammals. A good review of the evolution of DNA repair mechanisms themselves can be found Here, although it is a journal article and you may need an academic subscription to the journal (if you are a university student or staff you should be able to access it automatically if on a university network computer or you can access it through your libraries electronic resources.

Papers like this one also talk about this sort of thing.

Hope that helps and wasn't too long or dull!

Wednesday, May 28, 2008

From RNA To Humans

I would invite anyone who happens to stumble across this blog, as infrequently update as it is, to visit the link for videos from a symposium at The Rockefeller Institute titled: From RNA To Humans. Some really fascinating scientists gave talks, all of which are online, covering a wide range of topics in evolutionary biology. Interesting and Educational stuff.

Thursday, May 10, 2007

In The Light of Evolution

Today in the PNAS Early Edition the collected papers from the Colloquium entitled, In the Light of Evolution I: Adaptation and Complex Design, which was held on December 1st and 2nd of 2006, were released. These papers I think will be of special interest to those who follow the current Evolution and Anti-Evolution debate, ID "movement", etc. I have only started going through these papers, starting with the summary paper by Avise and Ayala which breaks down the papers into three topics: Epistemological Approaches To Biological Complexity, From Ontogeny to Symbiosis (A Hierarchy of Complexity), and Dissecting Complex Phenotypes (Case Studies).

It looks to be a good read as well as a good scientific summary of what Evolutionary Theory really has to say about areas that the ID enthusiasts and Creationists frequently like to misrepresent in their arguments. Papers will cover how natural processes give rise to complex systems, what is biological complexity and how can it be quantified?, ontogenic shifts and the emergence of new morphologies, etc. As I read papers in the series I will update with a sort of running commentary.

Tuesday, April 24, 2007


I haven't posted here in awhile, since I'm not exactly a blogger by nature and am thinking about turning this blog in to a sort of virtual journal club where a paper of interest is proposed weekly or bi-weekly and then people post comments discussing that paper. I don't think I have many regular readers but feedback would be appreciated.

Sunday, February 18, 2007

Can we remove the heirarchy of hypothesis from science education?

Repeatedly in my forays on the web, and in explaining science to non-scientists, in particular in the context of the ongoing evolution-creationism debates, I am constantly faced with explaining what a theory is in the context of science, and that the "hypothesis -> theory -> law" that many people no doubt learned in elementary and high school is simply wrong, and has been for a long, long time. Getting this erroneous thinking removed from the education process would go a long way towards improving the scientific literacy of people in general.