Upcoming lecture in Madison1
1. Coincidentally, Ms Sandwalk and I were just talking—less than 15 minutes ago— about how long it would take to drive to Madison from Toronto. I think we could do it in 12 hours.
1. Coincidentally, Ms Sandwalk and I were just talking—less than 15 minutes ago— about how long it would take to drive to Madison from Toronto. I think we could do it in 12 hours.
The assumption that science decided to leave out questions of god, meaning, purpose and value is a caricature of the history of science, and Haught, who claims to be making a serious attempt to show the compatibility of science and religion, must know this. If he doesn’t, and he really thinks that science made such a decision — how does “science” do this, by the way? — then his misunderstanding of the relation of science and religion is total.
When Haught turns around, then, and castigates Jerry by saying that everything that he said was a caricature, that every quotation that Jerry took from Haught’s work was taken out of context, and that instead of reading carefully and thoughtfully Jerry got his idea of god and theology from creationist websites, this was undoubtedly the most aggressive and impolite move of the whole debate. Listen to what he says:
I meant to say that broadly there are two types of people who call themselves atheists but only one really deserves the dignity of the term. The first category -- the peasant, clod, village atheist, am ha'aretz -- is the person like Jerry Coyne with a cartoon version in his head of some one religion or all religions. He rejects the cartoon, figuring that as far as faith goes in general, he's got it all figured out and it's all nonsense. This type of person typifies the New Atheist movement. He has very little of interest to say.Aren't you glad that you can get the best of the best by just reading David Klinghoffer on Evolution News & Views?
There's a second much rarer type, however, the person who has not only investigated at least one serious faith seriously but also experienced it, known believers, ideally was a believer himself at some adult stage of life. This person, in rejecting God, merits a real hearing.
From the Salvo Magazine interview with Jonathan Wells, by Casey Luskin. Wells is the author of The Myth of Junk DNA:Dear Jonathan Wells and Denyse O'Leary,
If you could have lunch with Francis Collins and Richard Dawkins, what would you say to them about their use of the “junk DNA” argument? [that there is no design in life]UD News does not think Collins would succeed. They are not Collins’s followers, they are Darwin’s men. They do not seek more knowledge than Darwin had. They seek to make what he knew part of the bedrock of Christianity.
Actually, Collins no longer relies on “junk DNA.” In 2007 he announced in an interview for Wired magazine that he had “stopped using the term.” In 2010 he wrote that “discoveries of the past decade, little known to most of the public, have completely overturned much of what used to be taught in high school biology. If you thought the DNA molecule comprised thousands of genes but far more ‘junk DNA,’ think again” (The Language of Life, pp. 5–6). Unfortunately, his followers at the BioLogos Institute (which he founded) seem to be unaware of this, because they continue to promote the myth that most of our DNA is junk. I would encourage Collins to set them right.
Unlike Collins, Dawkins seems utterly oblivious to recent developments in genomics. I would encourage him to read some of the scientific literature.Why? Dawkins can command international attention for not keeping up to date – because millions of tax burdens feel he speaks for them – and they don’t need to keep up to date either. Their champions are fronts for the dead orthodoxies that keep them in place.
An open Letter to Jerry Coyne:
Dear Jerry,
Your distorted reading of my motivation for not releasing the video of our conversation in Kentucky has given birth to an inordinate number of hostile letters to me. Because of misleading statements on your website (11/1/2011), I have received a considerable amount of hate mail, often laced with obscenities, though often also tempered with inquisitive politeness. The mail mostly complains about my “cowardly” reneging on an alleged agreement that you falsely assume I made to post online the video of our panel at the University of Kentucky. When I was in Kentucky I was never asked to do so. Later, after reflecting on what to me was a most unfortunate event, I wrote to Prof Rabel requesting that any video not be released.
Anyway, Jerry, your own words impute cowardice to me for this refusal, but how do you know that’s the reason for my reluctance? Here is a typical reaction stirred up by your remarks: “What a pathetic, sociopathic dweeb you are. Hiding behind your sick belief system you call a religion. You are an insult to academia, and a dim bulb for the uninformed masses. You deserve the insults you are getting and should be fired. Coward, liar and fool you are, loser. And no doubt a Republican too!” (I’m tempted to say that I can live with every accusation except the last.)
I want to make it clear that Rob Rabel at the University of Kentucky has confirmed that I never gave permission before or after the panel to post the video. You need to make this clear to your audience. I never broke the agreement that you have unkindly caused your readers to assume I made.
However, the more interesting issue has to do with my reasons for refusing permission to post the video, and whether it was wrong for me to do so. I have no regrets about anything I had to say during the panel, and if you agree to post this letter on your site I will be happy to have the video released unedited, for public scrutiny. Those who are reading this blog are free to look at other videos of my comments on science and religion available online. They will see that I have no need to hide my views from the public, and in fact I am quite eager to have my thoughts made available provided they are presented accurately and fairly.
Why then do I hesitate in this case? It has to do with you alone, Jerry, not anyone else, including myself. I have had wonderful conversations with many scientific skeptics over the years, but my meeting with you was exceptionally dismaying and unproductive. I mentioned to you personally already that in my view, the discussion in Kentucky seldom rose to the level of a truly academic encounter. I agree that it was probably entertaining to the audience who gave us a standing ovation at the end. Nevertheless, instead of being flattered by this I went away terribly discouraged at what had just taken place. I wish to emphasize that I do not exempt myself from criticism.
The event at the University of Kentucky did not take place in the way I had expected. My understanding was that each speaker was to provide a curt 25-minute presentation of how he understood the relationship between science and theology. I did just this, and I have no objection to having that presentation made public. People who attended the event, moreover, can testify that in my presentation I avoided talking about or criticizing you personally. Instead I was content to make some very general remarks about why I consider science completely compatible with theology as I understand it.
When Robert Rabel of the Gaines Center at the University of Kentucky, a true gentleman who remains far above reproach in all of this, contacted me last summer and invited me to participate in the event, he asked me for names of people who would differ from my own position. I recommended you as someone who would definitely have a different perspective, to say the least. Prof. Rabel informed me that you agreed to participate with the qualification that you did not want to debate me, but simply to lay out your own way of looking at science and religion. I took this to mean that you would do something parallel to what I did in my presentation.
Instead, you used the event primarily to launch a sneering and condescending ad hominem. Rather than using your 25 minutes as an opportunity to develop constructively your own belief that science and religion are always and inevitably in conflict, you were content simply to ridicule rather than refute several of my own ideas, as you interpreted them. On the other hand, my own presentation, as those who watch the video will see, was a dispassionate attempt to have the audience understand some of the reasons why the new scientific picture of the universe is so troubling to many traditionally religious people. I don’t believe that at any point in that presentation I resorted to ridicule, or that I focused on, much less misrepresented, anything you have written. Instead, I argued in a purely academic way that scientism is simply unreasonable. This was clearly my main point, and I was expecting you to respond to it in an academic manner as well.
Rather than answering my point that scientism is logically incoherent–which is really the main issue–and instead of addressing my argument that the encounter with religious truth requires personal transformation, or for that matter instead of responding to any of the other points I made, you were content to use most of your time to ridicule several isolated quotes from my books. I was absolutely astounded by your woeful lack of insight into, or willingness to grapple with, the real meaning of these passages. Sophisticated argument requires as an essential condition that you have the good manners to understand before you criticize. Your approach, on the other hand was simply one of “caricature and then crush.” Citation of a few isolated sentences or paragraphs, the meaning of which requires reading and understanding many chapters, is hardly useful criticism. You grossly distorted every quotation you used, and then you coated over your [mis]understanding of these statements with your own uncritical creationist and literalist set of assumptions about the Bible and theology. There was no room for real conversation, as impartial viewers will notice.
Instead of trying to convince the audience of the logical coherence and philosophical finality of your belief that science is the only reliable guide to truth, you began by arbitrarily announcing to the audience that John Haught is the chief representative of theology in the conversation of science with religion. You gave no evidence for that, and in fact it is by no means evidently true. I am but one of a great number of theologians involved in the discussion, and many others do not share my views. But your strategy was to show that if the principal figure is stupid, then you need not take his subordinates seriously either. This is a convenient method for shrinking the territory that needs to be covered, but it is hardly a fair way of dealing with all the other theological alternatives to your own belief system.
But let me come to the main reason why I have been reluctant to give permission to release the video. It is not for anything that I said during our encounter, but for a reason that I have never witnessed in public academic discussion before.
I’m still in shock at how your presentation ended up. I was so offended both personally and as an academic by the vulgarity of it all that I did not want other people to have to share what I witnessed that night in October. I still don’t.
I’m referring to the fact that your whole presentation ended up with a monstrous, not to mention tasteless, non sequitur, to give it the kindest possible characterization. You put on the screen a list of all the “evils” you associate with Catholicism: its stance regarding divorce, contraception, priest pedophilia, homosexuality–and I can’t remember what all–as though these have anything at all to do with the topic of the panel or with my own personal views on the relationship of science to theology. The whole focus of your presentation was on me, but when you came to your conclusion you never bothered to find out what my own position regarding your list of Catholic evils might be. I have never witnessed such a blatant smear or malicious attempt to impute guilt by association in all my years in university life.
Your list of Catholic evils, contrary to what you were suggesting, has absolutely nothing logically to contribute to your argument that science is opposed to religion. But even if it did, you never asked me whether I dissent from some or all the items on your list of “evils,” as many Catholics do, and whether such dissent might, in your twisted way of arguing, perhaps make my own position more credible. Your insinuation could only have been that somehow the priest sexual abuse crisis, for example, discredits my views on science and theology. You should be grateful that I have tried to protect the public from such a preposterous and logic-offending way of bringing your presentation to a close.
There is much more to be said, but this is all I will have to say to you or others on this matter. If you are willing to post this letter on your blog, go ahead and ask the Gaines Center to release the video as well. I have no objections now that I have had the opportunity to present my reservations to possible viewers.
Sincerely,
John Haught
1. I'm looking for articles from anyone who thinks that Haught did a good job of making the case for compatibility. Post a link in the comments.
2011 Bale Boone Symposium - Science & Religion: Are They Compatible? from UK Gaines Center on Vimeo.
Science and Religion: Are They Compatible? October 12, 2011 Q+A with Jerry Coyne and John Haught from UK College of Arts & Sciences on Vimeo.
1. There's a special treat in store for those who watch the Q&A. You will get to see an incredibly stupid first question from the moderator. I don't think I could have restrained myself the way Jerry Coyne did.
Q. Focusing on natural science, what is science?
A. Science is a mode of inquiry that looks to understand natural phenomena by looking for their natural causes, efficient and material causes. It does this by first gathering data observationally or empirically. Then it organizes this data into the form of hypotheses or theories. And then, thirdly, it continually tests the authenticity of these hypotheses and theories against new data that might come in and perhaps occasionally bring about the revision of the hypothesis or theory.
Alternative Splicing and Genome SizeI don't really understand the connection between alternative splicing and the C-value paradox. How does it explain why closely related species of onion have very different genome sizes?
A second point I made was that the phenomena of alternative splicing and alternative polyadenylation may have some explanatory power when it comes to accounting for the C-value enigma. Alternative splicing allows a single form of a pre-mRNA transcript to be spliced into a number of different forms by skipping exons or by recognizing alternative splice sites. I stated that the level of alternative splicing exhibited in humans (more than 90%, with an average of 2 or 3 transcripts per gene) is much higher than that for C. elegans (about 22%, with less than 2 transcripts per gene), and argued that this may, in part, explain why humans have only marginally more genes than C. elegans, which is otherwise seemingly paradoxical given the complexity of humans as compared to the roundworm.
On this point, Moran is not just in disagreement with me, he is also out-of-date with the literature by about ten years! As this 2008 article from Science Daily reports,I've written about IDiots and alternative splicing before, especially their inability to understand what they're talking about [Jonathan Wells Weighs in on Alternative Splicing]. But the issue here is somewhat different. It's whether the idea that most human genes are alternatively spliced is a scientific fact or whether it's controversial. Like most IDiots, Jonathan M doesn't understand the subject well enough to know the difference.
Nearly all human genes, about 94 percent, generate more than one form of their protein products, the team reports in the Nov. 2 online edition of Nature. Scientists' previous estimates ranged from a few percent 10 years ago to 50-plus percent more recently.Wang et al. (2008), moreover, report in Nature,
"A decade ago, alternative splicing of a gene was considered unusual, exotic ... but it turns out that's not true at all -- it's a nearly universal feature of human genes," said Christopher Burge, senior author of the paper and the Whitehead Career Development Associate Professor of Biology and Biological Engineering at MIT.
Through alternative processing of pre-messenger RNAs, individual mammalian genes often produce multiple mRNA and protein isoforms that may have related, distinct or even opposing functions. Here we report an in-depth analysis of 15 diverse human tissue and cell line transcriptomes on the basis of deep sequencing of complementary DNA fragments, yielding a digital inventory of gene and mRNA isoform expression. Analyses in which sequence reads are mapped to exon-exon junctions indicated that 92-94% of human genes undergo alternative splicing, ~86% with a minor isoform frequency of 15% or more.
Zhang et al. (2009)
Nonsense-mediated decay is a mechanism that degrades mRNAs with a premature termination codon. That some exons have premature termination codons at fixation is paradoxical: why make a transcript if it is only to be destroyed? One model supposes that splicing is inherently noisy and spurious transcripts are common. The evolution of a premature termination codon in a regularly made unwanted transcript can be a means to prevent costly translation. Alternatively, nonsense-mediated decay can be regulated under certain conditions so the presence of a premature termination codon can be a means to up-regulate transcripts needed when nonsense-mediated decay is suppressed....
We conclude that for recently evolved exons the noisy splicing model is the better explanation of their properties, while for ancient exons the nonsense-mediated decay regulated gene expression is a viable explanation.
Tress et al. (2007)
Alternative premessenger RNA splicing enables genes to generate more than one gene product. Splicing events that occur within protein coding regions have the potential to alter the biological function of the expressed protein and even to create new protein functions. Alternative splicing has been suggested as one explanation for the discrepancy between the number of human genes and functional complexity. Here, we carry out a detailed study of the alternatively spliced gene products annotated in the ENCODE pilot project. We find that alternative splicing in human genes is more frequent than has commonly been suggested, and we demonstrate that many of the potential alternative gene products will have markedly different structure and function from their constitutively spliced counterparts. For the vast majority of these alternative isoforms, little evidence exists to suggest they have a role as functional proteins, and it seems unlikely that the spectrum of conventional enzymatic or structural functions can be substantially extended through alternative splicing.
Melamud and Moult (2009)This is a controversial topic. Some of us believe that alternative splicing in human genes is not particularly widespread and most of the data can be explained as errors in splicing. Others believe that the data is real and most human genes produce multiple transcripts with different biological functions.
The number of known alternative human isoforms has been increasing steadily with the amount of available transcription data. To date, over 100 000 isoforms have been detected in EST libraries, and at least 75% of human genes have at least one alternative isoform. In this paper, we propose that most alternative splicing events are the result of noise in the splicing process. We show that the number of isoforms and their abundance can be predicted by a simple stochastic noise model that takes into account two factors: the number of introns in a gene and the expression level of a gene. The results strongly support the hypothesis that most alternative splicing is a consequence of stochastic noise in the splicing machinery, and has no functional significance. The results are also consistent with error rates tuned to ensure that an adequate level of functional product is produced and to reduce the toxic effect of accumulation of misfolding proteins. Based on simulation of sampling of virtual cDNA libraries, we estimate that error rates range from 1 to 10% depending on the number of introns and the expression level of a gene.
Melamud, E. and Moult, J. (2009) Stochastic noise in splicing machinery. Nucleic Acids Res. 37:4873-4886. [doi: 10.1093/nar/gkp471]
Pan, Q., Shai, O., Lee, L.J., Frey, B.J., and Blencowe, B.J. (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet. 2008 Dec;40(12):1413-5. Epub 2008 Nov 2. [doi:10.1038/ng.259]
Tress, M.L., Martelli, P.L., Frankish, A., Reeves, G.A., Wesselink, J.J,, Yeats, C., Olason, P.I., Albrecht, M., Hegyi, H., Giorgetti, A., Raimondo, D., Lagarde, J., Laskowski, R.A., López, G., Sadowski, M.I., Watsonk J.D., Fariselli, P., Rossi, I., Nagy, A., Kai, W., Størling, Z., Orsini, M., Assenov, Y., Blankenburg, H., Huthmacher, C., Ramírez, F., Schlicker, A., Denoeud, F., Jones, P., Kerrien, S., Orchard, S., Antonarakis, S.E., Reymond, A., Birney, E., Brunak, S., Casadio, R., Guigo, R., Harrow, J., Hermjakob, H., Jones, D.T., Lengauer, T., Orengo, C.A., Patthy, L., Thornton, J.M., Tramontano, A., and Valencia, A. (2007) The implications of alternative splicing in the ENCODE protein complement. Proc. Natl. Acad. Sci. USA 104:5495-5500. [doi: 10.1073/pnas.0700800104]
Zhang, Z., Xin, D., Wang, P., Zhou, L., Hu, L., Kong, X., and Hurst, L.D. (2009) Noisy splicing, more than expression regulation, explains why some exons are subject to nonsense-mediated mRNA decay. BMC Biol. 7:23-36. [doi:10.1186/1741-7007-7-23]
Briefly stated, the often cited "onion test" observes that onion cells have many times more DNA than human cells do. And since the onion is considered to be relatively simple as compared to us, this discrepancy -- it is argued -- can only be accounted for if the preponderance of its DNA is, in fact, junk or non-functional. Let's see whether the concept really holds any water.Let's go over this one more time. The Onion Test is a "test." (Look up the word "test" in the dictionary.) It's designed as a thought experiment to test a hypothesis about the possible function of large amounts of noncoding DNA. If you think you have an explanation for why most of the human genome has a function then you should explain how that accounts for the genomes of onions. Ryan Gregory knew that most so-called explanations look very silly when you try using them to account for genome size in onion species.
Each month, a fascinating hodge-podge of evolution-themed posts from blogs both big and small is collected in a single place and heralded far and wide. Or as far and wide as interested bloggers can herald it. Evolution is a broad topic with broad areas of agreement, some controversy (within the science itself), and regular surprises. So, if you're interested in evolutionary issues, post, tweet, text, or even speak the 41st CoE!The next Carnival of Evolution will be hosted by Psi Wavefunction at The Ocelloid. You can submit your articles for next month's carnival at Carnival of Evolution. Here's the website: Carnival of Evolution.
1. I put "high energy" in quotation marks because it's really the Gibbs free energy of the reaction (system) that we're referring to and not an individual molecule.
2. Rat liver biochemistry used to be very popular.
Alberty, R.A. and Goldberg, R.N. (1992) Standard thermodynamic formation properties of adenosie 5′-triphosphate series. Biochem. 31:10610-10615.