Uncommon Descent Serving The Intelligent Design Community

New! Evening news, new format, 5 items one post


1. Here’s a sure sign of a Darwinist losing an argument with the evidence: He (or she) rattles on that it will help “creationists.” It’s not like they care what the true story is or anything.

2. Remember Ben Carson? That brilliant neurosurgeon who sparked a Darwin hatefest at Emory University? He has a book out now, a bargain on Kindle at $4.63.

3. Decode ENCODE (= there is NOT much of the “junk” DNA Darwinists believed in) with embryologist Jonathan Wells Also ran: What Darwinists say about ENCODE (don’t seem knowledgeable) and Wells (“creationist clown”). This is what happens when you are right.

4. NCSE, the U.S. Darwin in the schools lobby, is really going big into climate change activism.

5. Obama vs. Romney on freedom of the Internet


1. Sure sign of Darwinist losing an argument with the evidence: He howls that it will help “creationists.” It’s not like he cares what the true story is or anything.

Here, molecular neurobiologist Athena Andreadis (“Junk DNA, Junky PR,” Scientific American, September 17, 2012), allows us to know,

Last but not least, the PR phrasing choices put wind in the sails of creationists and intelligent design (ID) adherents, by implying that everything in the genome has “a purpose under heaven”.

And that cannot be true, exactly why? There is nothing unusual about the idea of science having “armies of unalterable law.” It is only Darwinism that demands imperfection, messes, and mistakes, not science as such.

The pervasive but clearly erroneous take-home message of “a function for everything” harms biology among laypeople by implying ubiquitous purpose.

Well, maybe there is ubiquitous purpose. It is no part of science to say that there isn’t.

Of course, it’s funny to see creationists fall all over themselves to endorse the EP results while denying the entire foundation that gives raison d’être and context to such projects. As for ID adherents, they should spend some time datamining genome-encompassing results (microarray, SNP, genome-wide associated studies, deep sequencing and the like), to see how noisy and messy our genomes really are. I’d be happy to take volunteers for my microarray results, might as well use the eagerness to do real science!

Sorry, Athena, they’re busy with their own research. Find your own volunteers.

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2. Remember Ben Carson? That brilliant neurosurgeon who sparked a Darwin hatefest at Emory University? He has a book out now, a bargain on Kindle at $4.63. Here. It’s called America the Beautiful. Title of song?*

Here’s the story, including the U prez promising he will vet all speakers at his Indoctrinate U, no matter how accomplished, if they doubt Darwin. Here’s the outcome, where he spoke up against political correctness.

It’s sad to think of young people going into steep debt to sit at the feet of utter non-entities like the biology department at Emory U, thinking that they will somehow get a job out of it, only to discover that the world wants people who can do things.

* Yes! In another, more gracious age, some of us learned to sing that song in our “Geography – our World and Its Peoples” class


3. Decode ENCODE (there is not much “junk” DNA) with embryologist Jonathan Wells


Q. What’s significant about the ENCODE project and its findings?

A. The recent findings from ENCODE and related projects are significant for several reasons. First, the results from over a thousand experiments — involving dozens of laboratories and hundreds of scientists on three continents, published simultaneously in dozens of articles in five different journals — are remarkably consistent. Second, by providing abundant evidence that 80% or more of our DNA is functional, the results have greatly expanded our biological knowledge and may shed valuable light on some diseases. Third, the results demolish the argument used by Richard Dawkins and some other Darwinists that most of our DNA is “junk,” proving we could not have originated by design. As the journal Science put it, “Encode Project Writes Eulogy for Junk

Q. How did the Darwinist argument about “junk DNA” originate? Who coined the term, and why?

A. Francis Crick (who with James Watson unraveled the molecular structure of DNA in 1953) thought the significance of DNA lay in its ability to code for proteins. After biologists discovered that only about 2% of our DNA actually encodes proteins, Susumu Ohno and David Comings independently coined the term “junk DNA” in 1972 to refer to most of the remaining 98%. Some biologists (such as Thomas Cavalier-Smith and Gabriel Dover) thought we might eventually discover functions for non-protein-coding DNA, but others (including Kenneth R. Miller and Richard Dawkins) seized on the notion of junk DNA as evidence for Darwinian evolution and against intelligent design — since a designer would presumably not have filled our DNA with so much junk, but centuries of mutations might have.

– “Decoding ENCODE: A Q&A with Jonathan Wells,” (Evolution News & Views, September 24, 2012


But Darwinists can’t be wrong, just abusive. Which is okay because Darwin’s followers have been ruled by courts to be right. Or in charge. Or something. So meanwhile, back at Darwin’s bunker, we learn from University of Toronto evolutionary biologist Larry Moran,

My personal view is that none of them [consortium members] seem to be very knowledgeable about genome biology and the wrk [*sic*] that has been published over the past 40 years.

he thinks ENCODE is a “fiasco.” It would be, if you were him.

Meanwhile, Darwin’s trashhound P.Z. Myers responds to Jonathan Wells’ post on ENCODE:

Wells is a creationist clown notorious for his tortured abuse of the history of science. He doesn’t have a merely whiggish view of history — it’s more of a Burke&Hareish perspective, where if History isn’t conveniently dead to permit him to commit ghoulish atrocities on it, he’s willing to take a cosh to it’s skull and batter it into extinction. When Wells announces that he’s going to provide “historical context”, brace yourself for a graceless exercise in ugly alternative histories.

Wow. That’s on the level of Pasteur’s “omne vivum ex vivo” (all life comes from life) for sheer rhetorical power. Darwinism has a long way to go -in some direction or other – powered by this kind of support.

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4. NCSE, the U.S. Darwin in the schools lobby, is really going big into climate change activism.

Fresh batch of vids (9/28/2012) here, updates (9/21/2012) here (9/14/2012), and taking on new staff here. They are probably being funded by some concern to do all this, and it feels like the bulk of their work just at present. It’s tempting to suspect that they think Darwinism is a losing cause, and are jumping to something they hope will win. All the way down the page, climate change is a biggie there now.


5. Obama vs. Romney on freedom of the Internet

Recently, Scientific American’s editors asked fourteen questions (“Obama and Romney Tackle 14 Top Science Questions,” September 4, 2012) of the two candidates’s campaigns. Evolution did not come up, but freedom of the Internet did. That question should very much interest us. The Internet is key for the intelligent design community because it levels the ability to communicate, between elite groups who operate with taxpayer funding and those of us who raise our own support from what is left. And worldwide, there are ongoing efforts on the part of governments to assert control.

Anyway, have a look at the question, and the two responses, and see what you think:

9. The Internet. The Internet plays a central role in both our economy and our society. What role, if any, should the federal government play in managing the Internet to ensure its robust social, scientific, and economic role?

Barack Obama:

A free and open Internet is essential component of American society and of the modern economy. I support legislation to protect intellectual property online, but any effort to combat online piracy must not reduce freedom of expression, increase cybersecurity risk, or undermine the dynamic, innovative global Internet. I also believe it is essential that we take steps to strengthen our cybersecurity and ensure that we are guarding against threats to our vital information systems and critical infrastructure, all while preserving Americans’ privacy, data confidentiality, and civil liberties and recognizing the civilian nature of cyberspace.

Mitt Romney:

It is not the role of any government to “manage” the Internet. The Internet has flourished precisely because government has so far refrained from regulating this dynamic and essential cornerstone of our economy. I would rely primarily on innovation and market forces, not bureaucrats, to shape the Internet and maximize its economic, social and scientific value.

Thanks to the non-governmental multi-stakeholder model, the Internet is — and always has been — open to all ideas and lawful commerce as well as bountiful private investment. Unfortunately, President Obama has chosen to impose government as a central gatekeeper in the broadband economy. His policies interfere with the basic operation of the Internet, create uncertainty, and undermine investors and job creators.

Specifically, the FCC’s “Net Neutrality” regulation represents an Obama campaign promise fulfilled on behalf of certain special interests, but ultimately a “solution” in search of a problem. The government has now interjected itself in how networks will be constructed and managed, picked winners and losers in the marketplace, and determined how consumers will receive access to tomorrow’s new applications and services. The Obama Administration’s overreaching has replaced innovators and investors with Washington bureaucrats.

In addition to these domestic intrusions, there are also calls for increased international regulation of the Internet through the United Nations. I will oppose any effort to subject the Internet to an unaccountable, innovation-stifling international regulatory regime. Instead, I will clear away barriers to private investment and innovation and curtail needless regulation of the digital economy.

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Casey Luskin has a new article out on a new paper about gene sequence comparisons:
Common Ancestry: Wikipedia vs. the Data - Casey Luskin - October 5, 2012 Excerpt: In fact, the largest category of genes here is eukaryotic (cells with a nucleus) genes that have no homolog among prokaryotes (cells without a nucleus) -- they don't even have any possible candidate ancestors to explain where these genes came from, much less a consistent pattern of similarity pointing to one particular ancestor. All this is the opposite of "a direct correlation with common descent.",,, Syvanen, (in "Evolutionary Implications of Horizontal Gene Transfer," Annual Review of Genetics, Vol. 46:339-356 (2012), invokes widespread HGT (Horizontal Gene Transfer), but he's uncommonly honest about the data and its implications, offering the radical suggestion that "life might indeed have multiple origins.",,, let's now look within eukaryotes.,,, The biochemical organization of the innate immune systems of plants and animals is strikingly similar -- but this is a direct non-correlation with common descent. Thus, evolutionary scientists are forced to call them "unexpectedly similar," postulating that the similarities were "independently derived." This data is not explained by Darwinian evolution and common descent. It is explained by common design. Somehow, something tells me not to expect any corrections over at Wikipedia. http://www.evolutionnews.org/2012/10/common_ancestry_1065001.html
There’s been a lot of talk recently about the discussion on reddit concerning the ENCODE publicity fiasco.
If ENCODE publishes results, and the results pleases Darwinists, then Darwinists should be pleased as plums if it receives lots and lots of "publicity." So the fact that the "publicity" is a "fiasco", simply means that Darwinists are troubled by what ENCODE is reporting. The quote from Larry Moran that 'News' includes supports this very view. So, why then, are you bothering to make a distinction? Isn't it clear that Darwinists think the ENCODE "results" are a "fiasco"? Why try to distort the discomfort Darwinists feel by needlessly parsing words? (N.B. I know that 'News' has already accepted the 'clarification', but I think it is a 'clarification [distinction] without a difference.') PaV
OT: Overcome - Jeb Corliss http://www.youtube.com/watch?v=fStj3vPG5U8 bornagain77
This is just plain cool! Bacterium in a Laser Trap: Light Tube Can Grab and Scan Even Tiniest of Unicellular Organisms - (Oct. 4, 2012) Excerpt: Scientists from the Department of Microsystems Engineering (IMTEK) of the University of Freiburg have constructed an innovative new optical trap that can grab and scan tiny elongated bacteria with the help of a laser. The physicists Prof. Dr. Alexander Rohrbach und Matthias Koch created a kind of light tube that traps the agile unicellular organisms. Optical tweezers could previously only be used to grab bacteria at one point, not to manipulate their orientation. The Freiburg researchers have now succeeded in using a quickly moving, focused laser beam to exert an equally distributed force over the entire bacterium, which constantly changes its complex form. At the same time, they were able to record the movements of the trapped bacterium in high-speed three-dimensional images by measuring miniscule deflections of the light particles. http://www.sciencedaily.com/releases/2012/10/121004104052.htm bornagain77
OT: The ghost of Paley's Watch comes back with a vengeance to haunt Darwinists: Study find electricity in biological clock - October 4, 2012 Excerpt: "This process helps explain how our biological clocks keep such amazingly good time," said Justin Blau,,,, In a previous study, Blau and his colleagues found that rhythms in expression of a potassium channel (Ir) helps link the biological clock to the activity of pacemaker neurons. But Ir does not function as a simple output of the clock—it also feeds back to regulate the core clock. In the Current Biology research, the scientists sought to understand the nature of this feedback.,,, By manipulating the neuronal activity of pacemaker neurons, the researchers showed that changes in the electrical activity of clock neurons produce major changes in the expression of circadian genes.,,, In other words, the electrical state of a clock neuron can dramatically affect circadian gene expression in clock neurons.,,, "What was striking about these results was the coordination between the firing of neurons and gene expression," observed Blau. "This is one of the remarkable processes that helps keep clock neurons stay synchronized and run so accurately.",,, "These data really make us focus on 'the clock' as a neuronal system rather than a set of genes," noted Blau. http://phys.org/news/2012-10-electricity-biological-clock.html bornagain77
I LOVE IT! “a purpose under heaven”. To hear them quoting scripture, in spite of themselves! But isn't it beautiful when they acknowledge the truth of so much eminently serviceable DNA, now empirically proven to be so, while admitting to being scared of its power to undermine their religion. Kind of warriors to protect falsehood, on (ir)religious grounds. '“Well, maybe it’s technically functional,” they say, “but it really isn’t.”,,, And isn't it so lovably human to prefer 'old wives' tales' to technical, scientific data? Axel
Thanks for clariff re Larry Moran's view, timothya. IfMoran thinks so little of the ENCODE team's abilities, it's a wonder he doesn't thiink the whole thing a fiasco. - News News
OT: David Berlinski at "Socrates in the City" speaking on 'Einstein's Blunder' - podcast http://intelligentdesign.podomatic.com/entry/2012-10-03T17_34_17-07_00 bornagain77
as to:
He also objects to the redefinition of the term “functional” in a fashion that makes it virtually useless as a diagnostic of biological activity.
Why the Case for Junk DNA 2.0 Still Fails - September 27, 2012 Excerpt: Confronted with the ENCODE results that attribute "function" to at least 80% of the genome, some Darwinist bloggers and critics of intelligent design have established a defensive perimeter around the precious idea of Junk DNA. It truly is that critically important to them. Their favored critique of ENCODE -- call it the case for Junk DNA 2.0 -- is that ENCODE's definition of functionality is wrong. "Well, maybe it's technically functional," they say, "but it really isn't.",,, As Jonathan Wells documented in Chapter 7 of The Myth of Junk DNA, we already know of several non-biochemical functions of non-protein-coding DNA,,, if anything, ENCODE uses too narrow a definition of function -- by limiting it to "biochemical" function. For this reason, the (80%) functionality reported by ENCODE surely underestimates the total.,,, http://www.evolutionnews.org/2012/09/why_the_case_fo_1064771.html Junk No More: ENCODE Project Nature Paper Finds "Biochemical Functions for 80% of the Genome" - Casey Luskin September 5, 2012 Excerpt: The Discover Magazine article further explains that the rest of the 20% of the genome is likely to have function as well: "And what's in the remaining 20 percent? Possibly not junk either, according to Ewan Birney, the project's Lead Analysis Coordinator and self-described "cat-herder-in-chief". He explains that ENCODE only (!) looked at 147 types of cells, and the human body has a few thousand. A given part of the genome might control a gene in one cell type, but not others. If every cell is included, functions may emerge for the phantom proportion. "It's likely that 80 percent will go to 100 percent," says Birney. "We don't really have any large chunks of redundant DNA. This metaphor of junk isn't that useful."" http://www.evolutionnews.org/2012/09/junk_no_more_en_1064001.html ENCODE: The Encyclopedia of DNA Elements (Interviews with members of the ENCODE Project) - video http://www.youtube.com/watch?v=PsV_sEDSE2o Quotes from preceding video: "Very little of our genomes are junk. 80% of our genome is engaged in at least one biochemical activity. For a large fraction of our genome, not now 5%, but 80% of the genome, we can (now) say that we know that it does something." "This metaphor about Junk DNA has become very entrenched. It has been entrenched publicly and entrenched scientifically. And ENCODE totally challenges that. We just don't have big, blank, boring, bits of the genome. All the genome is alive at some level." "There are about 2000 DNA binding proteins in the genome. We looked at about 100 of those, 115 of those, so there is a long way to go yet, there is a lot more to study." What Is The Genome? It's Certainly Not Junk! - Dr. Robert Carter - video - (Notes in video description) http://www.metacafe.com/w/8905583
I wonder if the 2012 ENCODE research did a call graph comparing the Transcription Regulation network in humans to a Call Graph of a computer operating system as the preceding video did for e-coli? It would certainly be very interesting to see the comparative differences between the e-coli and the human Transcription Regulation networks since humans have a vastly more expansive regulatory network than e-coli does.
Global project reveals just how active our 'junk' DNA is - Sept. 2012 Excerpt: They found that, across the genome, about 19 per cent of our DNA may code for RNA switches that turn genes on or off. "We see way more switches than we were expecting, and nearly every part of the genome is close to a switch," project coordinator Ewan Birney of the European Bioinformatics Institute in Cambridge, UK, told New Scientist. The switches also appear to be spread out over the genome, with some being located at a distance from the gene they are controlling. Around 95 per cent of the genome appears to be very close to a switch, suggesting that almost all of our DNA may be doing something important. http://www.newscientist.com/blogs/shortsharpscience/2012/09/global-project-reveals-what-ou.html “Millions of DNA Switches That Power Human Genome’s Operating System Are Discovered.” - Sept. 2012 http://www.sciencedaily.com/releases/2012/09/120905135326.htm Time to Redefine the Concept of a Gene? - Sept. 10, 2012 Excerpt: As detailed in my second post on alternative splicing, there is one human gene that codes for 576 different proteins, and there is one fruit fly gene that codes for 38,016 different proteins! While the fact that a single gene can code for so many proteins is truly astounding, we didn’t really know how prevalent alternative splicing is. Are there only a few genes that participate in it, or do most genes engage in it? The ENCODE data presented in reference 2 indicates that at least 75% of all genes participate in alternative splicing. They also indicate that the number of different proteins each gene makes varies significantly, with most genes producing somewhere between 2 and 25. Based on these results, it seems clear that the RNA transcripts are the real carriers of genetic information. This is why some members of the ENCODE team are arguing that an RNA transcript, not a gene, should be considered the fundamental unit of inheritance. http://networkedblogs.com/BYdo8 The Extreme Complexity Of Genes – Dr. Raymond G. Bohlin – video http://www.metacafe.com/watch/8593991/
News claimed this concerning Larry Moran:
. . . he thinks ENCODE is a “fiasco.” It would be, if you were him.
No he didn't. From the blog post you linked to, he said this:
There's been a lot of talk recently about the discussion on reddit concerning the ENCODE publicity fiasco. [emphasis added]
It is the overblown public relations claims made by the program leadership to which he objects mightily. In my humble opinion, he is correct. He also objects to the redefinition of the term "functional" in a fashion that makes it virtually useless as a diagnostic of biological activity. timothya
#5 Lubos Motl did an interesting review of the science questions a while back here: http://motls.blogspot.com/2012/09/science-debate-14-questions-romney.html?m=1 Eric Anderson

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