UF Walkout for Peace on 3/20; Red Dawn Analogy

Activism:

Join the UF Walkout for Peace with the Students for a Democratic Society in Gainesville. See the Facebook event for more, and use it to invite friends. For me, it doesn't impact any classes or anything, since I'm a grad student.

On that note, I read a very poignant take on Iraq, using the comparison to the film Red Dawn, by Jim Downey. His major point is that rightwingers love that movie, and the ideals it embodies, but fail completely to apply that perspective to Iraq:

But what gets me is the complete disconnect that occurs with those on the right when it comes to applying the ostensible lessons of the movie to the real world, and specifically to Iraq. Red Dawn is all about how Americans would resist an invasion, even unto death, and is glorified on the right for this reason. People don't take kindly to being "ruled" by outside invaders or illegitimate government. Why on earth do the Republicans who still support this war think that the Iraqi people are any different from us in this regard?

Perhaps that's just it - early on the rhetoric was how we would be 'bringing democracy' to Iraq, and the repressed Iraqis would welcome us and quickly adopt our ways, because all people yearn to be free. But now the notion is that the Iraqis are somehow different from us in this regard, 'less' than us, and all we have to do is to continue to occupy their country long enough, with enough troops, as we did to the evil Germans and Japanese after WWII.

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Technorati tags: Politics

On the Origin of the Genetic Code and Abiogenesis

**Update (11/25/07): See here for updated links for all the papers below**

A new research paper in Science demonstrates yet more evidence for abiogenesis -- finally a 3D map of the chemical structure of a beautiful example of a ribozyme, one which researchers built "from scratch" and could very easily have evolved naturally under the right chemical conditions. See the EurekAlert!, and a perspective on the research:

No known RNA enzyme in biology catalyzes the polymerase-like joining of RNA. However, the powerful methods of in vitro evolution have made it possible to generate such enzymes from scratch, starting from a large population of RNAs with random sequences (6). The usual approach is first to evolve an RNA enzyme that is an RNA ligase, which can join two oligonucleotides in a template-directed manner. Then, through further evolution, the researcher attempts to coax the ligase to accept NTPs as substrates and to add multiple NTPs in succession.

Bartel and colleagues (7) have used one such in vitro evolved ligase, the class I ligase, and evolved it further to polymerize as many as 14 successive NTPs with high fidelity. Despite valiant efforts, however, it appears unlikely that this particular polymerase enzyme will ever be evolved to the point that it can copy RNA molecules as long as itself (~200 nucleotides). Nonetheless, it is likely that scientists will eventually apply a similar approach to a different set of RNA molecules to achieve more extensive polymerization and ultimately complete replication.

As the gaps in our knowledge continue to close, the "god of the gaps" continues to shrink along with them. This is as true today of the "Intelligent Design" creationism movement as it was of Young Earth Creationists and their pseudo-scientific arguments against evolutionary biology.

A very recent case-in-point is shown by Dr. Michael Egnor's rejection of evolution on the basis of a half-baked conception of evolution's inability to generate biological "information," which I refuted with peer-reviewed resources here. After reading Orac shredding the fallacies propounded by Dr. Michael Egnor, and especially the, "Duh, I don't know or understand this, so it must not be true!" (classic argumentum ad ignorantium), I wanted to highlight his section on the origin of the genetic code:

I'll agree that how the genetic code evolved is indeed a very good scientific question, but it is a question that in no way poses a threat to current evolutionary theory or requires the postulation of some sort of intelligence to explain. Indeed, it's a hot topic of research for evolutionary biologists, with computer simulations evaluating the plausibility of various explanations and competing hypotheses being tested scientifically. If you search PubMed, you'll find over 5,000 articles about or touching on the evolution of the genetic code, and PubMed doesn't even index many evolutionary biology journals in which such articles would be expected to appear. Indeed, there was a rather interesting paper in PNAS in November about how the universal genetic code may have emerged as determined by studying of transfer RNAs. It also seems to me that Egnor also sounds almost Lamarckian in the way he describes how animals evolve thicker coats in response to cold climate. He also seems not to have considered that the very fact that the genetic code is very nearly universal for all organisms can also be viewed as supporting evolution. If the development of the genetic code appeared very early in the history of life, that would go a long way towards explaining why nearly all life, from bacteria to humans, uses the same code, and even the variants of the genetic code that exist are minor.

Indeed. In addition to these papers, I wanted to highlight six other recent reviews that give a great overview of the present scientific thinking towards the origin of the genetic code:

1. "Selection, history and chemistry: the three faces of the genetic code.", Trends in Biochemical Sciences, Volume 24, Issue 6, 1 June 1999, Pages 241-247 (full-text .pdf)
   
2. "Genetic code: Lucky chance or fundamental law of nature?", Physics of Life Reviews, Volume 1, Issue 3, Dec 2004, Pages 202-229 (full-text .pdf) [low-quality pub, but expansive overview of the subject]
   
3. "Stepwise Evolution of Nonliving to Living Chemical Systems.", Origins of Life and Evolution of the Biosphere, Volume 34, Issue 4, Aug 2004, Pages 371–389 (full-text .pdf)
4. "The Origin of Cellular Life.", Bioessays, Volume 22, Issue 12, Dec 2004, Pages 1160-1170 (full-text .pdf)
5. "The Origin of the Genetic Code: Theories and Their Relationships, A Review.", Biosystems, Volume 80, Issue 2, May 2005, Pages 175-184 (full-text .pdf)
6. "The Origin and Evolution of the Genetic Code: Statistical and Experimental Investigations.", Robin D. Knight, Ph.D. Dissertation, June 2001.
   

There are answers. Do the creationists know that they exist? Mostly not. Would they understand them if they did? Mostly not. How much knowledge is required before creationists admit that we have sound scientific answers to all of their objections? There will never be enough. Ever.

The bar of evidence would continue to be elevated, just as Behe demonstrated with respect to the immune system (blood clotting cascade = BCC, irreducible complexity = IC):

The BCC arguments can be found throughout IDC websites. One of the most well-informed responders to these arguments is Andrea Bottaro. Last year, as more evidence came in that transposons were involved in the human immune response, Dr. Bottaro put together the pieces and completely refuted the claim of IC as it applies to BCC. How did Prof. Behe respond? By moving the goalposts -- not in any way denying the evidence, but demanding a mutation-by-mutation account of the pathways involved. Thus, he undercuts his own argument by rendering the burden of proof unattainable by any scientific pursuit.

Creationists will continue to place ridiculous burdens of proof upon science, while completely refusing to provide positive evidence of their own (because, of course, they have none). Their arguments are, 99.9% of the time, anti-evolutionary in nature, because there are no sound pro-creationism arguments. And, as Judge Jones articulately pointed out, this fallacy of logic is the false dilemma: "If you're wrong, then I'm right."

The court in McLean stated that creation science rested on a "contrived dualism" that recognized only two possible explanations for life, the scientific theory of evolution and biblical creationism, treated the two as mutually exclusive such that "one must either accept the literal interpretation of Genesis or else believe in the godless system of evolution," and accordingly viewed any critiques of evolution as evidence that necessarily supported biblical creationism.

Typical creationist stupidity.

What knowledge do they produce? What cures do they offer? What technology have they manufactured? None. Nada. Zilch. They deal only in ignorance. They give nothing in the way of evidence or argument, and ask for the world in return. When mountains of evidence are presented to them, like in the papers above, they ignore them and dodge the facts entirely.

All they offer are bad arguments against evolution, distortions of facts, and philosophical pleas based on unsound premises. Their desperation is evidenced clearly by the depths to which they descend in order to preserve their silly superstitious religious beliefs. And desperate they ought to be, because evolution has irreparably demolished the validity of the ancient creationist myths forever.
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Technorati tags: Intelligent Design, Evolution, Creationism

A Little Feedback on My Talk with Todd Friel

As I mentioned, I talked to Todd Friel on "Way of the Master Radio," and he aired my segment. Well, I got some feedback.

A nice fellow, a college student at Boyce College in Louisville, KY, has edited the segment down to the relevant portion -- about 15 mins worth, and you can listen to it here on Odeo or download it here. After reading his feedback, I left a comment on his site.

I am the atheist who called in to talk to Todd, and as I explained on my website, I used a pseudonym. You can read what I had to say about it already here if you like.

He extensively edited our talk, but I understand why -- we talked for about 40 mins. He cut out the parts about evolution and cosmology (the Standard Model, or the "Big Bang" if you prefer), and he cut out some of the end.

Now, I'm a little confused by what you wrote:

It also shows that Atheists can deny God, but when it all boils down to it - you still have to deal with that “Sin” thing.

Atheists don't "deny God" per se, they don't believe in God.

People do not always behave as they ought. Now, how do we go from there to "however, there is a God," or even, "however, there is a judgment"?? Please, feel free to show me how that is an inevitable (or even a logical) conclusion...

I hope he replies. Upon listening to a little bit of the clip, I smiled at Todd's belief that atheists equivocate over the term "atheist". Todd is blissfully ignorant, it appears, that atheists have been arguing amongst themselves for years about what "weak atheism" versus "strong atheism" is, and whether someone can be an agnostic atheist, etc.

Todd thinks it's "all about deconstruction" -- he seems blissfully unaware that many (if not the huge majority of) atheists are not post-modernists. For me it is quite simple:

• I cannot disbelieve, or claim to know, anything about a concept which is not defined
• Therefore, define "god" for me, and then I'll explain whether I claim to believe or know something about it
• I am thus an agnostic about god-concepts that are vague or undefined, but an atheist about many defined and well-known gods, like the Christian god and Allah and Thor...
  
• If "god" = "the Western God, omni³: all-knowing, all-powerful, all-loving", then I will unequivocally not only admit to disbelief, but also I will claim that such a God doesn't exist, because of arguments like these and these
• If "god" = "the power of love" or "the grounding of existence", then I'll roll my eyes and walk away.
  

Seems simple enough to me.
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Technorati tags: God, Religion, Atheism, Philosophy

Proud of the NEA

I'm quite proud of the National Evangelical Association for being more than a lap dog of the Religious Right and standing up for human rights and the environment, against the tide of criticism from Dobson and groups like the Family Research Council. I just hope they continue to do so. I don't think this controversy should be thought of as a "family feud," because I don't think the RR has any family -- the unholy alliance of conservative politics with fundamentalist Christianity so far has no bastard spawn (pure fascism) nor friendly cousins in liberal religion (all conscientious liberals reject this movement, regardless of shared religious views).

I've written before about the rift between Evangelicals and the RR, and I hope to see it continue to widen as the former grows in concern for broader issues (how about poverty, peace, and Darfur, just for starters?), and the latter is increasingly marginalized and trivialized by its own stupidity. I hope.

See: NYT, CNN, DefCon
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Technorati tags: Religion, Politics

Study Finds that Scripture Inspires Aggression in Students

A scientific study published in the March issue of the journal Psychological Science and mentioned in Nature found that students exposed to invocations of violence responded more aggressively when it was from a religious context. Undergraduates from both BYU (n = 248) and from a university in Amsterdam (n = 242) -- Vrije Universiteit -- were studied.

The lead author, Prof. Brad Bushman, made the publications (linked above) available from his website.

Does this surprise anyone? When you're told to hurt others, nothing removes inhibition like the feeling of being on a divinely-inspired mission. History and common sense confirm that.
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Technorati tags: God, Religion

FFRF's "Freethought of the Day": Einstein

Being a member of the FFRF entitles you to the email service "Freethought of the Day" -- receiving interetsing biographical and historical information on famous freethinkers each day. Today's date had two freethinkers, one a little more famous than the other: Judge Arnold Krekel and Albert Einstein. I want to reproduce the section on Einstein below...it's worth it.

Albert Einstein

On this date in 1879, Albert Einstein was born in Germany. He completed his Ph.D. at the University of Zurich by 1909. His 1905 paper explaining the photo-electric effect, the basis of electronics, earned him the Nobel Prize in 1921. His first paper on Special Relativity Theory, also published in 1905, changed the world. Einstein split his time and academic appointments between various European universities. In 1932, Princeton named him head of the Mathematics Department, and he traveled back and forth between the continents. After the rise of the Nazi party, Einstein made Princeton his permanent home, becoming a U.S. citizen in 1940. Einstein, a pacifist during World War I, stayed a firm proponent of social justice and responsibility. He chaired the Emergency Committee of Atomic Scientists, which organized to alert the public to the dangers of atomic warfare.

In an article for The New York Times (Nov. 9, 1930), Einstein wrote about his views on religion, and wonder at the cosmic mysteries: "This insight into the mystery of life, coupled though it be with fear, also has given rise to religion. To know that what is impenetrable to us really exists, manifesting itself as the highest wisdom and the most radiant beauty which our dull faculties can comprehend only in their primitive forms--this knowledge, this feeling, is at the center of true religiousness. In this sense, and in this sense only, I belong in the ranks of devoutly religious men."

Confusion over his beliefs stemmed from such comments as his public statement, reported by United Press in April 25, 1929, that: "I believe in Spinoza's God, who reveals himself in the orderly harmony in being, not in God who deals with the facts and actions of men." Einstein's famous "God does not play dice with the Universe" metaphor--meaning nature conforms to mathematical law--fueled more confusion.

At a symposium, he advised: "In their struggle for the ethical good, teachers of religion must have the stature to give up the doctrine of a personal God, that is, give up that source of fear and hope which in the past placed such vast power in the hands of priests. In their labors they will have to avail themselves of those forces which are capable of cultivating the Good, the True, and the Beautiful in humanity itself. This is, to be sure a more difficult but an incomparably more worthy task. . . ." ("Science, Philosophy and Religion, A Symposium," published by the Conference on Science, Philosophy and Religion in their Relation to the Democratic Way of Life, Inc., New York, 1941). D. 1955.

“I cannot imagine a God who rewards and punishes the objects of his creation, whose purposes are modeled after our own--a God, in short, who is but a reflection of human frailty. Neither can I believe that the individual survives the death of his body, although feeble souls harbor such thoughts through fear or ridiculous egotism. It is enough for me to contemplate the mystery of conscious life perpetuating itself through all eternity, to reflect upon the marvelous structure of the universe which we can dimly perceive, and to try humbly to comprehend even an infinitesimal part of the intelligence manifested in nature.”
-- Albert Einstein, column for The New York Times, Nov. 9, 1930 (reprinted in The New York Times obituary, April 19, 1955)

Wonderful words. I've written before on how theists try to distort Einstein's true beliefs into their own in a lame appeal to authority, in order to prop up the credence of god-belief. And, did you know that I own an Albert Einstein action figure? Jealous, aren't you?
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Technorati tags: God, Religion, Philosophy

On "Way of the Master Radio" with Todd Friel

Out of boredom and curiosity, I called in to Way of the Master Radio on Friday evening. The host, Todd Friel, will be debating Eddie in Daytona Beach on 3/26, and I'm hoping he'll be able to come here the day before to do our debate. He's one of the last on my list as potential opponents.

I called in as "David" from Tampa, 23, at UF studying chemistry. I simply used a pseudonym because I wasn't sure how the show would go -- if he would be hostile, if he would even air my segment. I was also a little insecure about being live on air, and I've never debated live on-air before, so I wanted to see how it went. Only the beginning of my call was captured at the very end of the second hour of Friday's show, but he taped the rest of it and promised to air it later (on Monday, I suppose). You can listen to the last 2 minutes of the show here and catch me being welcomed on.

___*UPDATE*___

He did indeed put it on Monday's show, hour 2. You can listen to it here. My segment with him starts about 40 minutes in. He did a lot of editing of the show, which doesn't surprise me very much, and it is hard to tell, but he is actually jumping in and out of the show with explanations, and cutting out parts, rather than just letting it all play.

For instance, he completely omitted the part about cosmology and how the Standard Model = "something from nothing," where I corrected him and called him on equivocation.

One big thing that Todd messes up badly is the idea that atheists are "suppressing knowledge of God" in order to deny the judgment. I've dealt with this at some length before, and the problem with this argument, as I tried to point out, is that I don't have to deny a god's existence in order to deny the Christian God's existence, or in order to deny the Bible's inerrancy, etc. It is a non sequitur of the highest order to say, "If God, then judgment," yet Todd seems to take this leap in logic for granted and as if it is self-evident! The God of the Deists is only one of thousands of completely accessible theistic beliefs that avoid the whole notion of orthodox Christian judgment, along with Islam and Hinduism and etc. To say that atheists "just disbelieve to avoid judgment" is thus laughable.

At the end of the show, notice that he dodged the issue of mercy vs. justice entirely. Like many Christians, he can't seem to comprehend that you cannot both be merciful and just at the same time:

Mercy: Not giving someone what they deserve
Just: Giving someone what they deserve

According to Todd, at the end of the show, God is always just. He always gives people what they deserve. However, with the same breath, and in complete self-contradiction, he claims that all sinners deserve hell, but that some do not receive it, because they "repent and trust"...

The argument is that because God punished Himself, an innocent Person, in order to give mercy, it is still just, because someone "paid for" what I deserve.

So, in this twisted view of justice, an innocent person can be punished for a guilty person's crimes, and this is still just!! No. That is complete rubbish. Instead, this would be barbaric and injust. Now, if the person who is punished volunteers to be punished, then you have mercy, not justice. And if God can be merciful to whomever he pleases, and accept their wrongdoings by forgiving them for those wrongdoings, then of course God can arbitrarily decide to be merciful at his own whim! As Paul said in Romans 9:15-31ff, this sort of God just decides who to have mercy on, and who to judge justly, and can make some people for hell, and some for heaven ("vessels fit for destruction, vessels fit for mercy").

Of course, the question of how the whole "hell = just punishment for sin" argument follows, even if God does put people in hell, is a completely separate, and even more difficult, issue.

DagoodS from DC has dealt with this issue at some length: God gets to make the rules, and one of the rules can be that he doesn't have to enforce them at all times, and thus God gets to decide what justice is and what mercy is. The whole idea that God is "bound" to throw sinners into hell is thus laughable and absurd.

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One other thing to highlight: Exapologist points to a new and useful resource on the Christian apologetic commonly known as "presuppositionalism". I have covered this issue at some length here and elsewhere, and Prof. Witmer's intro to the subject, and his interview with Gene Cook, is always a good place to start.
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Technorati tags: God, Religion, Atheism