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Entropic Existence

Home of my musings and ramblings on Molecular Evolution, Computational Biology, Whacky Science, and occasionally banal day-to-day affairs.

Updated: 2016-09-08T01:27:36.652-03:00


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.[...]

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[...]

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 [...]

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.(image)

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.(image)



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.(image)

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.(image)

Benny Hinn eXtreme!!


Ok so this really has nothing to do with science, although I could write a length diatribe on the mental state of the fervently religious, the power of persuasion, and of course the con that goes into all of this evangelical faith healing but mostly I just wanted to link to this video because it is hilarious. Benny Hinn faith healing + appropriate rock music = priceless.(image)

Another article from an ID supporter that raises my hackles


Recently (thanks to I came across this article in the Guardian from across the pond. Some of the article makes a degree of sense (as many of these ID articles do) but for someone who has supposedly worked in the field Mr. Buggs seems to make an awfuly lot of mistakes concerning evolution. Of course when I do a pubmed search for Buggs, R the results are a little slim. Three articles in pubmed and only one is truly in an evolution journal.

I think my "favourite" paragraph from the article was the following:

Science has turned lots of corners since Darwin, and many of them have thrown up data quite unpredicted by his theory. Who, on Darwinian premises, would have expected that the patterns of distribution and abundance of species in tropical rainforests could be modelled without taking local adaptation into account? Or that whenever we sequence a new genome we find unique genes, unlike any found in other species? Or that bacteria gain pathogenicity (the ability to cause disease) by losing genes?

Ok so for the first point on modeling species distributions and species abundance I'm not sure what models he is referring to, nor what they use as input parameters. And of course I am not an ecologist but I do know that those sorts of things follow probabilistic distributions of one sort or another, and I am willing to bet that input parameters for those models DO take adaptation/evolution into account somehow, even if it is via proxy. (For example if you are modeling the distribution of a predator one typically includes prey distributions in the model. That actually does take evolution/adaptation into account by proxy).

As for the second, bacteria losing genes to gain pathogenicity I have to wonder if Mr. Buggs has ever heard of Pathogenicity Islands. Those wonderful little groups of genes that get swapped via Lateral Gene Transfer like crazy among bacteria.

I am forced to conclude that Mr. Buggs credentials are either over sold in relation to the topic at hand, or like so many others in the ID posse, he deliberately bends the truth in order to sway public opinion.(image)

Pattern Matching


I've been thinking about pattern matching a lot lately in the context of the human brain and evolution after originally being sparked to the idea over at the The Evolution List some time ago. When you start thinking about it you realize just how much pattern matching can explain some elements of religious belief and the supernatural. Back when our ancestors where barely upright and living on the fringe of the forest and Savannah in Africa pattern matching was a key component of survival. Signs that would indicate a predator was nearby, signs of the weather, etc. But like many things in nature pattern matching is balanced on a very delicate knife's edge. Too strong and you start having a heart attack every time you see your own shadow, too lenient and that lion has you for dinner. But overall it pays too be a little too jumpy than to be too lenient, and so humans have a tendency to see things that aren't there. Couple that with consciousness and high intelligence and one can imagine all sorts of funny things happening.

It is also amazing how well written science fiction can sometimes be. As a student of the sciences I have a guilty love for sci-fi, but it can often be a love hate relationship. After all frequently so many sci-fi books are just plain wrong on many levels, especially when it comes to topics related to molecular biology. I can't fault the authors too much after all, they write for their audience and their audience is generally not very well versed in that subject matter anyway. Recently I came across this book by a Canadian author called Blindsight. Mr. Watts has a background in marine biology and so he can tackle this hard sci-fi novel from a well researched scientific perspective, in fact he even includes a well written appendix at the end discussing some of the scientific issues in his book such as consciousness in the light of evolution and just what the advantages and disadvantages of a conscious mind really are. He is also rather generous in providing citations to his reference material, most of which are peer-reviewed articles from Science and Nature.

I highly recommend the book, I found it quite enjoyable although it is one of those books that is hard to get lost in. The pacing tends to be a little slow but it is highly interesting and gets you hooked. Definitely an interesting look at the differences between intelligence and consciousness as well as a fascinating exploration of the idea of human-alien contact. Technology implies belligerence.(image)

First Post


Well I maintained a personal blog at one time, but it wasn't something that interested me that much. I've decided to maintain this blog targeted more generally at things in science that interest me.

I am currently working towards my Masters in Computational Biology and Bioinformatics with an interest in making predictions about proteins based on their sequence using an evolutionary approach.

As you can see my interests are rather broad, with my research being very interdisciplinary in nature. Hopefully I will keep up with this little experiment, posting and commenting on issues relating to science, evolution, molecular biology, and computational biology.(image)