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Monthly Archives: October 2008

There are a number of scientists who I greatly admire not only for the work in their fields but because they also apply their intellect to humanity. Some, like Nikolai Vavilov and Robert Oppenheimer, were persecuted by their own governments for their anti-establishment views.

Vavilov, a prominent Russian evolutionary biologist, lost his life opposing Trofim Lysenko, whose Lamarckism-based agrarian policies killed millions of Soviet citizens from famine after disastrous crop failures. Vavilov saw the need for protecting the future of humanity by collecting seeds of all crop species of plant and protecting their gene lines. We owe him far more than we realize as the genetic lines of almost all of our current grain crops can be traced to the repository Vavilov set up with his foresight. For openly opposing Lysenko he was starved to death in an internment camp in Stalin’s Russia. 

Oppenheimer spoke out vehemently against proliferation of the very weapon he helped to create as head of the Manhattan Project. In thanks, the very politicians which brought us all to the brink of nuclear holocaust numerous times stripped Oppenheimer of his security clearance in a very public kangaroo court during the big Red Hunt of the 50’s.

Nobel laureate Physicist Stephen Weinberg is another of those applying his intellect to what I call ‘the Big Questions’ of life, the universe and everything. The following is a cut-and-paste entry retrieved from Enjoy!

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One of the primary arguments for the value of Religion is its moral guidance. Benjamin Franklin once stated that

religion will be a powerful regulator of our actions, give us peace and tranquility within our minds, and render us benevolent, useful and beneficial to others…1

He was right, but not at all for the reason he would have thought. Not only do I think that Religion is unnecessary as a moral guide, it actually enables good people to perform evil acts by suspending normal moral boundaries with the excuse that harming fellow humans is secondary to obeying God. My central thesis is that Religion is no guarantor of good behavior, let alone a source of morality, and any perceived association between the two is totally manufactured to serve the interests of those promoting their belief system.

The US is arguably the most religious nation in the developed world, yet it also leads or is no different from more secular countries in rates of nonviolent and non-lethal violent crime2, homicide3, adolescent suicide4, teen pregnancy5 and teen STD transmission6. I do not argue that Religion is the root cause of the first three in this list, but I will argue in a later segue (Religion and Politics) that it is a significant factor (if not the single major factor) in the last two items. Yet many Believers would have us accept that the solution to such social problems is yet more religious belief when it is abundantly clear that it has far too much of a negative effect on society with vastly insufficient positive compensatory traits.

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‘The Bible is not my book nor Christianity my profession. I could never give assent to the long, complicated statements of Christian dogma.’ ~ Abraham Lincoln

A lot of Christians think they are being singled out when religion is criticized. In North America, this is actually true. But it’s not because we atheists have some soft spot for any other religion. It’s certainly not because atheists and agnostics in this part of the world think Christianity is somehow less credible than other mythologies. It’s simply because Christianity is what we are familiar with. Not surprising, given the relevant demographics on this continent. I just know more about it to criticize the specific elements of the religion. If I knew more about Judaism and Islam I would be equally critical in the specifics of their tenets.

And from what I do know about other religions, I see the same withdrawal from reason as that demonstrated by practitioners of Christianity. I see no reason to accept that any religion is more valid than any other. I’m very equal-opportunity in that regard. All religions ask one thing: either accept or reject unsubstantiated and unverifiable dogma. Given such a choice the path is clear: I do not. In the absence of positive evidence to the contrary, logic demands that the null hypothesis (in this case, the non-existence of god(s)) be maintained.

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The concept of Irreducible Complexity (IC) and, by extension Intelligent Design (ID) as a whole, is a defeatest and slothful concept. It’s proponents whine and wail that things are too complicated to have arisen through blind natural processes so don’t even bother to try to understand it. What kind of attitude is that? If everyone in history had this outlook we would still be throwing rocks to catch dinner. Science as we know it arose because there were those who did not accept that dogmatically-given answers are immune from being questioned. In other words, what we know as modern Science arose in spite of Religion and most definitely not because of it.

And – trust me on this – I did not need the opinon of Judge Jones III, as correct as it was, to know that ID is NOT Science. In Science, we deal in explanations that offer insight into the mechanisms of processes, not simply substituting another expression for “I don’t know”, like “a magic man done it”, and trying to pass it off as somehow being a satisfactory answer when it answers exactly nothing. How do we know when something is ‘too complex’ except when given as a ‘just so’ story? And ‘just so’ stories are as dogmatic as it gets. In Science we systematically work to divest ourselves of dogma, not embrace it!

In the Kitzmiller v. Dover case, Dr. Michael Behe was front and center for the defense trying to put forward the idea that this idiotic concept ‘explains’ the complexity of cellular structures that he feels (without ever presenting any data to corroborate his belief) could not come to be through the blind machinations of natural selection.

Poppycock. Behe tries to appeal to ignorance, which is not a logical argument at all. This is true in every single example supposedly supporting IC he has ever given. But his argument is never any more than throwing up his hands in self-fulfilling defeat at a real explanation. At the Kitzmiller trial, he was forced to admit that he was not even familliar with the relevant literature! This is the height of intellectual dishonesty, and because Behe espouses such nonsense his colleagues have completely (and rightly) disowned these nonsensical ideas (and let’s face it – him). This underscores a basic difference between ID (or should I say ‘cdesign proponentsists’?) and Evolution proponents in that the latter actually work to gather evidence in support of hypotheses while the former do nothing but sponge off the gullible by telling the faithful what they want to hear.

Today I’m going to discuss what proponents of ID consider the poster child for their position and why it is really far-and-away better represented by evolution.

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In our species, this offshoot desire to answer the Burning Questions has resulted in what Daniel Dennett calls ‘premature curiosity satisfaction’. Like other premature events, it is actually undesirable. The more philosophically minded believers realized the need to create arguments to buttress their presupposition that God exists. This is not an admirable methodology. Certainly, in my vocation, such a procedure where the conclusion is the starting point rather than the end point is more than just frowned upon. It leads to rationalization, which becomes quite apparent in the many philosophical arguments.

I am a metaphysical naturalist. I used to consider myself a methodological naturalist, but I came to realize that admitting the possibility of something outside of a naturalist universe in the utter absence of any indication that such is the case is intellectually dishonest. So I have taken the plunge and gone all the way. This does not mean that if extraordinary evidence that there is some phenomena which can only be explained outside of naturalism that I would not change my position. But in the complete paucity of extraordinary evidence to the contrary, to consider anything outside of naturalism in order to explain phenomena is a complete waste of time.

As such, I am no fan of philosophical arguments unsupported by empirical evidence. Science has a habit of squashing them like grapes in a winery. Nicholas Everitt, when writing a book on arguments for the existence of God, gave up and just titled the book The Non-existence of God. As he describes, there are simply no good philosophical arguments for the existence of deities.

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Every molecule in your body has a story to tell. This tale is about hemoglobin, the class of oxygen-binding molecules that make oxygen transport in complex creatures such as us possible. Hemoglobins are proteins that contain the heme moiety, a planar molecule binding iron (Fe) and maintaining it in the +2 oxidataion state (denoted Fe(II)).

Hemoglogins in the Animal Kingdom
Hemoglobins in almost all vertebrates is a heterotetramer (that is, four (‘tetra’) individual of different (‘hetero’) proteins) composed of two α-globin and two β-globin polypeptides (a fancy word for proteins). The heme part is bound in a pocket formed by structure of each globin unit. The movement and interactions between the subunits increases hemoglobin’s ability to bind oxygen.

Hemoglobin structure

Hemoglobin structure

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Of late a lot of hubbub has brewed over Richard Lenski’s latest paper on the laboratory evolution of citrate-eating E. coli (PNAS 105(23):7899-7906 (2008)). Lenski figures very prominently in Carl Zimmer’s overview of E. coli research entitled Microcosm, and for good reason. For those that don’t know of the content of the current paper, for the last 20 years Lenski and his students have been growing bacteria (starting from a single bacterium and creating 12 lines) and periodically freezing samples (every 500 generations or so) to see if these bacteria evolve in the lab. At the time this paper was published, over 44,000 generations had passed.

Periodically, the frozen ‘fossil’ bacteria can be thawed and DNA compared over time. Since the bacteria are cloned and reproduce asexually, only natural selection and genetic drift can act on the gene populations, greatly simplifying analysis. Previous to this paper, changes in growth rates, reduced lag phases when the bacteria were transfered to a fresh culture medium, reduced peak population densities and larger cell sizes relative to their ancestors were reported. Most populations evolved increased DNA supercoiling.

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The web blogsite MySpace does not have a Science section. I find that rather insulting, being a scientist. The world makes use of the benefits of Science to such an extent that the MySpace gods are completely oblivious to their dependence on it. In a sense, this jaded attitude is in part responsible for the rise of pseudoscience and spirituality. In my book, a spiritual person is a flake. Where does Deepak Chopra get off telling us that scientists have hijacked the term ‘quantum mechanics’ as if it were spiritual gurus and not physicists that were its developers? He’s got it backwards! It is HE that has hijacked it and made it out to be something which it is most definitely not. Quantum healing my ass! What a rube. Anyway, this article is cut and pasted from the Australian Skeptics website and is an excellent discussion on Shannon information and the increase in information in the genome. Why don’t creationists get it? This is so much more fascinating than the banal god-dunn-it!

Speaking of them, why are they so dishonest when going out to interview scientists? PZ Myers ran into the same problem when Ben Stein filmed that train wreck. I’ll lay money down that Richard is totally up front with his motives. Creationist propagandists, on the other hand, always seem to use underhanded tactics.


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Some time ago, PBS aired an episode of Nova entitled ‘Judgement Day’. It was, in my estimation, an excellent discussion of what went on in the town of Dover when creationists attempted to inject their inanity about how life came to be into a Science class.  I highly recommend watching it, as it was an accurate depiction of what went on in the subsequent lawsuit.  And, yes, I have read both the trial transcripts and the judge’s decision, so I am in a position to make such a judgement call. 

The program re-enacted a number of highlights from the trial. Michael Behe, the only member of the Discovery Institute of those originally scheduled to appear, was supposed to be the defence’s star witness. It turned out he was an unwitting wringer for the prosecution. Behe is an example of one of the most interesting properties of creationists (or intelligent design) proponents: their inability to change their ideas in the face of overwhelming evidence. Behe has been repeatedly told why his concept of ‘irreducible complexity’ and the examples he gives for it are completely bogus, yet he has never changed his tune. And this was why he was totally demolished on the witness stand. Of course, Behe produced his pet example of irreducible complexity, the bacterial flagellum.

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This is an updated repost of a blog I posted last year about a man with Huntington’s disease. The audio feed can be found on The Current (Part II). After a few comments in another blog entry on the biological evidence of homosexual behavior vs the silly notion of it being a ‘lifestyle choice’, I thought about this entry. Not all genetic testing is bad, but I agree we are starting to wade into a moral quagmire.

Huntington’s disease is a neurodegenerative disorder with profound cognitive and motor disturbances, and typically kills its victim about 10 to 15 years after symptoms become manifest. Onset occurs in midlife, typically after victims have started their own families and possibly passed the gene on to the next generation. The chances of one parent with the gene passing it on to any one child is 50%.

The Human Genome Project has provided some hope, at least potential hope, of a cure for this terrible disorder. Certainly, it has allowed genetic testing of embryos for the Huntington’s gene, and tests for some 200 genetic disorders exist at present. One Canadian researcher, Jeff Carroll, has a vested interest in finding a cure- he has the disease himself. The remainder of the embryos were made available for research into a cure for Huntington’s.

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