A dose of humility re:junk DNA?

On Junk DNA Claim, Francis Collins Walks It Back, Admitting "Hubris"

David Klinghoffer

Count on Marvin Olasky at World Magazine not to miss something like this. In The Language of God, theistic evolutionary icon Francis Collins used so-called Junk DNA as homerun evidence against intelligent design. He has since backed down on that, honorably, admitting "hubris" in the process. Olasky:

Collins claimed on page 136 that huge chunks of our genome are "littered" with ancient repetitive elements (AREs), so that "roughly 45 percent of the human genome [is] made up of such genetic flotsam and jetsam." In his talk he claimed the existence of "junk DNA" was proof that man and mice had a common ancestor, because God would not have created man with useless genes.

Last year, though, speaking at the J.P. Morgan Healthcare Conference in San Francisco, Collins threw in the towel: "In terms of junk DNA, we don't use that term anymore because I think it was pretty much a case of hubris to imagine that we could dispense with any part of the genome, as if we knew enough to say it wasn't functional. ... Most of the genome that we used to think was there for spacer turns out to be doing stuff."

Good for Collins -- and maybe he'll go on to deal with other times scientists feel sorry for God as they look at His purportedly poor design. For example, evolutionists use the retina of the eye as evidence against creation, because nerve endings are at the front rather than at the back, which at first glance seems better placement. Yet, as Lee Spetner explains in The Evolution Revolution (Judaica Press, 2014), physicists now see front placement as the best one for "ingeniously designed light collectors."

The list of needed retractions should include what you probably learned in high school about apparently purposeless human vestigial organs. Robert Wiedersheim's 1895 list of 86 has shrunk, as almost all of them have proved to have functions. For example, the most famous vestigial organ -- the vermiform appendix -- is a crucial storage place for benign bacteria that repopulate the gut when diarrhea strikes. The appendix can be a life-saver.

By "hubris" perhaps he means the overweening tendency to assume that scientific opinion as constituted at the moment has got everything all figured out. The repeated need to retract and walk back previous certainties should be a lesson to all, a warning that we can't simply hand over our intellects to "science."

In briefest form, that's the message of Doug Axe's book Undeniable. When it comes to big-ticket science questions like evolution, not only do you get to think for yourself. You have a positive obligation to do so.

Why we need not idolise science for it to be of value.

Yes, There Can Be Science Without Scientism, and Without Relativism
Sarah Chaffee


In an article at Slate referring to Neil deGrasse Tyson's now famous #Rationalia tweet, sociologist Jeffery Guhin argues that "A rational nation ruled by science would be a terrible idea."

What? This, from popular media? Guhin makes his case against scientism, noting:

First, experts usually don't know nearly as much as they think they do....[T]he real problem is when we forget that scientists and experts are human too, and approach evidence and reasoned deliberation with the same prior commitments and unspoken assumptions as anyone else. Scientists: they're just like us.

Yes -- science, like any other human enterprise, is flawed.

"And second, science has no business telling people how to live," Guhin continues. Decrying scientific racism, he recalls that "Eugenics was science, as was social Darwinism and the worst justifications of the Soviet and Nazi regimes." Kudos to Guhin for recognizing that -- a point that many other commentators avoid facing squarely.

In fact, that sounds remarkably like what Discovery Institute's John G. West says in Darwin Day in America: How Our Politics and Culture Have Been Dehumanized in the Name of Science. As Dr. West summarizes in the Preface:

At the dawn of the last century, leading scientists and politicians giddily predicted that modern science -- especially Darwinian biology -- would supply solutions to all the intractable problems of American society, from crime to poverty to sexual maladjustment.

Instead, politics and culture were dehumanized as a new generation of "scientific" experts began treating human beings as little more than animals or machines:

In criminal justice, these experts denied the existence of free will and proposed replacing punishment with invasive "cures" such as the lobotomy.

In welfare, they proposed eliminating the poor by sterilizing those deemed biologically unfit.

In business, they urged the selection of workers based on racist theories of human evolution and the development of advertising methods to more effectively manipulate consumer behavior.

In sex education, they advocated creating a new sexual morality based on "normal mammalian behavior," without regard to longstanding ethical or religious imperatives.

But here Guhin abruptly changes direction with a weird foray into bashing creationism. He says that "creationism has a lot more in common with scientism than people such as Tyson or Richard Dawkins would ever admit." Where did that come from? My guess is it's tactical. At Slate, to get away with saying anything that could be seen as critical of materialism, you need to demonstrate your credibility by attacking the creationists.

He has no strong conclusion to his article; rather Guhin's last section is entitled "The elusive truth." Once creationism and scientism are gone, it turns out, what's left is relativism. He says, "Science may give us data, but it doesn't mean that data points to truth -- it's just what we currently understand as truth."

True, there's no science without faith, as Douglas Axe notes in Undeniable:

Science can't even conceivably give us anything more certain than the faith we place in the essential propositions undergirding science, which means science will never be the primary path to knowing, much less the only path to knowing.

But is there a third way? Can we reject the confines of pure materialism without rejecting the information-value of data? Can there be science without scientism?

Historically, science existed in a non-materialist framework. Intelligent design, unlike Darwinian evolution, provides a basis for believing that we are able to ascertain truth about the world while recognizing that some things may be beyond science's reach. ID aligns wells with a view affirming that humans are unique and it is consonant with the existence of ultimate meaning. At the same time, it affirms the importance of rationality and science -- which can help us to improve our quality of life through healthcare, technology, and more.


Accepting reality does not mean throwing away rationality -- just #Rationalia.

Scientists comment on "undeniable."

More Scientists Praise Douglas Axe's Undeniable
David Klinghoffer 

One of the refreshing things about Doug Axe's new book  Undeniable: How Biology Confirms Our Intuition That Life Is Designed is his confession that you don't have to take his word for it. Or anyone else's, for that matter.Despite being a molecular biologist who has done the lab research to confirm the impossibility of unguided nature chancing upon functional proteins, he shows how, even without that, the design intuition most of us share embodies sound science.

We don't need to rely slavishly on what scientists say because, in an important sense, we are all scientists, capable of judging a big scientific idea like evolution, if not necessarily the technical details, for ourselves. Evolution's defenders in the world of science love to overawe the public with those details, but we can look past and through them. Its defenders in the media tend toward a precious, almost worshipful regard for scientists, but as Dr. Axe reminds us, professionals in the sciences are human just like us.

All that having been said, it's interesting to hear from those professionals -- biologists especially -- who agree with Dr. Axe on his main point. And indeed endorsements for the book have continued to come in.

From Russell W. Carlson, Professor Emeritus, Department of Biochemistry and Molecular Biology, University of Georgia:

Many say we must accept that life is ultimately due to a grand cosmic accident, that evolution is an unguided purposeless process, and that we must deny our experience. Axe describes why the design we see in nature fits with scientific observation as well as with our "undeniable" experience.

From Matti Leisola, D.Sc., Professor Emeritus of Bioprocess Engineering, Aalto University, Finland:

Douglas Axe is one of the very few experimental scientists who has used his skills to test the validity of evolutionary mechanisms as a source of inventions. Here, he concludes that we can trust our common (universal) design intuition; it is supported by science, whereas evolutionary stories are anti-science.

From Mark C. Biedebach, Professor Emeritus, Department of Biological Sciences, California State University, Long Beach:

In Undeniable, Dr. Axe has carefully crafted a case that strongly favors our human intuition that life was designed. As a protein chemist, he gives numerous examples and reasons why unguided evolution (even of a cell's protein molecules) is improbable in the extreme. As I understand his case, its power to convince surpasses that of anything else I have ever read (on origins science) during my 65 years as an engineer, biophysicist, and physiologist.

Whoa. Frankly, those endorsements would be impressive from any scholar, or any thoughtful adult. They're all the more so from scientists who, you would have to agree even against your will (if you're a Darwinist), know what they're talking about.

Time for true separation of church and state in the U.K?Pros and cons.

A clash of titans XXIV

(Not so)Civil war?

When Atheists Attack (Each Other)
David Klinghoffer 

The squabble between Darwin lobbyists who openly hate religion and those who only quietly disdain it grows ever more personal, bitter and pathetic. On one side, evangelizing New or "Gnu" (ha ha) Atheists like Jerry Coyne and his acolytes at Why Evolution Is True. Dr. Coyne is a biologist who teaches and ostensibly researches at the University of Chicago but has a heck of a lot of free time on his hands for blogging and posting pictures of cute cats.

On the other side, so-called accommodationists like the crowd at the National Center for Science Education, who attack the New Atheists for the political offense of being rude to religious believers and supposedly messing up the alliance between religious and irreligious Darwinists.

I say "supposedly" because there's no evidence any substantial body of opinion is actually being changed on religion or evolution by anything the open haters or the quiet disdainers say. Everyone seems to seriously think they're either going to defeat religion, or merely "creationism," or both by blogging for an audience of fellow Darwinists.

Want to see what I mean? This is all pretty strictly a battle of stinkbugs in a bottle. Try to follow it without getting a headache.

Coyne recently drew excited applause from fellow biologist-atheist-blogger PZ Myers for Coyne's "open letter" (published on his blog) to the NCSE and its British equivalent, the British Centre for Science Education. In the letter, Coyne took umbrage at criticism of the New Atheists, mostly on blogs, emanating from the two accommodationist organizations. He vowed that,

We will continue to answer the misguided attacks [on the New Atheists] by people like Josh Rosenau, Roger Stanyard, and Nick Matzke so long as they keep mounting those attacks.
Like the NCSE, the BCSE seeks to pump up Darwin in the public mind without scaring religious people. This guy called Stanyard at the BCSE complains of losing a night's sleep over the nastiness of the rhetoric on Coyne's blog. Coyne in turn complained that Stanyard complained that a blog commenter complained that Nick Matzke, formerly of the NCSE, is like "vermin." Coyne also hit out at blogger Jason Rosenhouse for an "epic"-length blog post complaining of New Atheist "incivility." In the blog, Rosenhouse, who teaches math at James Madison University, wrote an update about how he had revised an insulting comment about the NCSE's Josh Rosenau that he, Rosenhouse, made in a previous version of the post.
That last bit briefly confused me. In occasionally skimming the writings of Jason Rosenhouse and Josh Rosenau in the past, I realized now I had been assuming they were the same person. They are not!

It goes on and on. In the course of his own blog post, Professor Coyne disavowed name-calling and berated Stanyard (remember him? The British guy) for "glomming onto" the Matzke-vermin insult like "white on rice, or Kwok on a Leica." What's a Kwok? Not a what but a who -- John Kwok, presumably a pseudonym, one of the most tirelessly obsessive commenters on Darwinist blog sites. Besides lashing at intelligent design, he often writes of his interest in photographic gear such as a camera by Leica. I have the impression that Kwok irritates even fellow Darwinists.

There's no need to keep all the names straight in your head. I certainly can't. I'm only taking your time, recounting just a small part of one confused exchange, to illustrate the culture of these Darwinists who write so impassionedly about religion, whether for abolishing it or befriending it. Writes Coyne in reply to Stanyard,

I'd suggest, then, that you lay off telling us what to do until you've read about our goals. The fact is that we'll always be fighting creationism until religion goes away, and when it does the fight will be over, as it is in Scandinavia.
A skeptic might suggest that turning America into Scandinavia, as far as religion goes, is an outsized goal, more like a delusion, for this group as they sit hunched over their computers shooting intemperate comments back and forth at each other all day. Or in poor Stanyard's case, all night.
There's a feverish, terrarium-like and oxygen-starved quality to this world of online Darwinists and atheists. It could only be sustained by the isolation of the Internet. They don't seem to realize that the public accepts Darwinism to the extent it does -- which is not much -- primarily because of what William James would call the sheer, simple "prestige" that the opinion grants. Arguments and evidence have little to do with it.

The prestige of Darwinism is not going to be affected by how the battle between Jerry Coyne and the NCSE turns out. New Atheist arguments are hobbled by the same isolation from what people think and feel. I have not yet read anything by any of these gentlemen or ladies, whether the open haters or the quiet disdainers, that conveys anything like a real comprehension of religious feeling or thought.


Even as they fight over the most effective way to relate to "religion," the open atheists and the accomodationists speak of an abstraction, a cartoon, that no actual religious person would recognize. No one is going to be persuaded if he doesn't already wish to be persuaded for other personal reasons. No faith is under threat from the likes of Jerry Coyne.

Enzymes v.Darwin.

When Enzymes Don't Lie
Evolution News & Views 

New research published in Bio-Complexity calls into question some fundamental assumptions of neo-Darwinian theory and enzyme evolution.

Enzymes are proteins that catalyze reactions that are necessary for life. Enzymes play such a fundamental role in life that many researchers are interested in how they originated and how they have evolved. They are composed of strings of amino acids, and the particular sequence of amino acids determines what three-dimensional shape each protein has, and what enzymatic function it carries out. Biologists categorize enzymes into families based on similarity of structure. The more similar the structure, the closer the evolutionary relationship is presumed to be.

It is generally believed that these enzyme families arose by a process of gene duplication followed by divergence of the extra copies over time. If accumulating mutations in an extra gene led to a beneficial change in enzyme function, the gene encoding that enzyme would tend to be preserved. Over time, then, repeated rounds of duplication and divergence would produce the large multi-functional families we see today. Yet for this explanation to be true, converting enzymes to new functions must require only a few mutations in order for the process to be within reach of neo-Darwinian evolution.

Doug Axe and Ann Gauger from Biologic Institute recently published a paper that addresses this pervasive assumption about the ease of enzyme conversion :
Here, we explore this question by asking how many mutations are needed to achieve a genuine functional conversion in a case where the necessary structural change is known to be small relative to the change commonly attributed to paralogous divergence.

As the authors report, they focused "not on minor functional adjustments, like shifts in substrate profiles, but rather on true innovations -- the jumps to new chemistry that must have happened but which seem to defy gradualistic explanation." Their aim was not to establish ancestry between two particular enzymes, but to identify a functional innovation that should be relatively straightforward within a superfamily and then evaluate how evolutionarily feasible this modest innovation would be.
They began by looking at a large "superfamily" known as the pyridoxal-5'-phosphate (PLP) dependent transferases. This is a well-characterized family of enzymes that share a common fold (shape) but catalyze distinctly different reactions. They identified a pair within that superfamily with very close structural similarity but no functional overlap. Kbl2 is involved in threonine (a type of amino acid) metabolism, and BioF2 is part of the biotin biosynthesis pathway. They then used a three-stage process to identify the sequences mostly likely to confer a functional change.

The experimental question is: How many mutations are required to convert Kbl to BioF function?

Experimental Results:
There are about 250 different amino-acid differences between Kbl and BioF. This is a huge number, and probably many more than the minimum number of amino acids that are needed to convert one enzyme's function to the other's. In order to determine the minimum number of amino acid changes necessary for functional innovation to occur, Gauger and Axe followed a three stage process. First they used sequence and structural comparisons of the two enzymes to identify candidate amino acids most likely to be significant for function. Second, they mutated those amino acids in BioF, making them like Kbl, and checked for loss of BioF activity. They identified three groups of amino acids, each consisting of six or seven individual amino acids, and one single amino acid, H152, that were essential for BioF function. Finally, they tested whether changing these groups in Kbl to look like BioF would enable the mutated Kbl to substitute for BioF.

The experiment ended up showing that no functional conversion could be achieved, even when all identified changes were made, including every amino acid in the enzyme's active site (the place where the enzyme's chemistry is carried out). Gauger and Axe estimate that seven or more mutations would be required to convert Kbl to BioF function.

So what does this all mean?

Two major implications need to be noted from the results of this experiment. In a second post, we will have a further discussion on implications of this research for neo-Darwinism.

The first finding was that H152 was vital to the functionality of the BioF. Perhaps what is most interesting about this finding is that H152 is not within the active site but is on the enzyme surface away from the active site. It is generally believed that the active site is the area of interest for enzymes within a family and the rest of the enzyme (the "scaffold") just holds the active site. However, these experimental findings seem to indicate that the non-active site differences, however minimal they may be, need to be considered, and that these differences may be more important than the apparent similarities.

The second implication from this failure to convert functionality is the question of whether a neo-Darwinian process of step-by-step conversion from one enzyme to another is actually feasible. The two enzymes in this study were very similar enzymes, yet even with generous estimates for mutation rate, gene duplication rate, and no fitness cost for carrying the extra gene, there does not seem to be enough time for mutations of this sort to occur:

"...seven is a reasonable lower-bound estimate of the specific nucleotide substitutions required for conversion...this places the Kbl [to] BioF conversion outside the bounds of what can be achieved by the Darwinian mechanism." When using the established mechanisms and estimates, it would require 10^30 or more generations to elapse before any type of BioF-like conversion could be established. There is not enough time to accomplish this relatively small innovation! As Axe and Gauger aptly summarize:
This places the innovation well beyond what can be expected within the time that life has existed on earth, under favorable assumptions. In fact, even the unrealistically favorable assumption that kbl duplicates carry no fitness cost leaves the conversion just beyond the limits of feasibility.


These are not large leaps or large-scale changes, but small-scale changes. And other research, cited in this paper, have shown the same difficulty in achieving enzyme conversions. This calls into question a fundamental assumption in the neo-Darwinian paradigm, that similarity of structure or form means ease of conversion, and implies that a different paradigm is necessary to account for enzymatic functional conversion.

Spiders in the dock for design.

Spiders Have Eight (Well-Designed) Eyes
Evolution News & Views

Have you ever wanted eyes in the back of your head? Spiders have eight eyes, compared to our two. They can boast of better vision than ours on some counts; sharp, color vision that extends into the ultraviolet. Their ample set of peepers allows for division of labor: the main pair in front helps them see detail, while the smaller eyes wrapped around their heads warn them of looming threats. Stephanie Pappas wrote about spider eyes on Live Science recently.

"We see that division of labor within that visual system... That's pretty cool if you think about it, because we only have one pair of eyes."
That was actually a quote from Skye Long, a doctoral student at the University of Massachusetts at Amherst, who decided to test and find out what the extra eyes are for. She outfitted an enclosure for her 46 jumping spider subjects and used paint to "blindfold" the principal eyes on a third of them, and the adjacent, smaller eyes (anterior lateral pair) on another third, leaving one third blindfold-free. (Don't worry about the spiders; the paint could be easily removed.)
Then she used an iPod Touch to create images of a black dot growing or shrinking in size. When seeing the "looming threat," the spiders backed up quickly and raised their front legs in defense, as if they felt scared -- even when the principal eyes were covered. This means the anterior lateral pair are crucial for alerting the spider to potential dangers. What are the other four eyes used for? That's what Long wants to find out next.

This would have been a "pretty cool" Halloween animal story, featuring a nice, experimental science project, had not Skye Long wandered off into evolutionary tale-telling:

That means the secondary eyes are crucial for alerting the spider to dangerous motion, Long said. Spider eyes are a "really cool step in evolution," she added; insects have compound eyes with multiple lenses, and some areas of those eyes have certain functions. Spiders, on the other hand, separate out visual functions across their heads.
"This is a different pathway that evolution has taken to allow a very small animal to have a very extensive visual system," Long said.

Right. No matter how cool or well-designed the adaption, just say it evolved. It's a "really cool step in evolution." It's a "different pathway evolution has taken." The blind, aimless, purposeless process of natural selection gave spiders a "very extensive visual system." Turn in your paper and get an A.
Here's a better way. Look what researchers at the Optical Society of America are doing with spiders. Incredible as it sounds, they are taking spider silk and using it for fiber optics. Spider silk is already prized as an ideal material: it's strong, flexible, and biodegradable. Now, a team has found it can also transmit and guide light almost as well as glass fibers.

One team is using it as a light guide in photonic chips, while another is trying to imitate the proteins in silk from spiders and silkworms to be able to manufacture it. This second team has already made a silk-based "plastic" that can be used for everything from biodegradable cups to implantable devices that dissolve in the body. Fiorenzo Omenetto presented his work in a superb TED Talk that raised the audience to their feet without him once mentioning evolution. And he is getting grants from the NSF!


Evolution is a straw scarecrow whenever it appears in biological research. The whole story is intelligent design, in the animals and plants studied, in the experiments devised to gain knowledge about them, and in the applications they lead to. Animal tricks become science's treats.

The winged flocks v Darwin.

Starling Murmurations and Intelligent Design, Revisited
David Klinghoffer




A friend points out the bit of nice news that one of our favorite nature video clips, "‪Dylan Winter and the Starling Murmurations," from the Illustra film Flight: The Genius of Birds, has exceeded a million views on YouTube. Not bad. That's a million plus people exposed to one of the most remarkable demonstrations of the wonders of bird flight.

All those viewers may not know precisely how starling murmurations give evidence of intelligent design. We've discussed this in the past:

"Why Starling Murmurations Suggest Intelligent Design"

"'Not By Chance': Drone Engineers Try the Starling Trick"

"Fly Now; Swim Later"

As Dr. Timothy Standish explained, here in a nutshell is the challenge posed by starling murmurations to traditional evolutionary thinking:

In the cold hard world of survival of the fittest, starlings that stick with the group may enhance their odds of surviving predation. But such an effect is an emergent property of the murmuration. Attributing the origin of murmurations to enhanced survival requires first that murmurations exist, thus making for a circular argument. To circumvent this problem, a Darwinist might invoke cooption. Maybe the ancestors of modern starlings gathered together for some other practical purpose and then, in a lucky coincidence, gained the survival advantage provided by murmurations. But think about the resources consumed by daily migrations followed by considerable time flying about with other starlings. It's unclear why any other proposed reason for investing resources this way would not be equally vulnerable to the criticism of circularity.

Flying in formation has advantages that humans quickly recognized once we mastered powered flight. The most obvious of these involves multiple sets of eyes looking out for enemies or obstacles. If human intelligence can figure this out, perhaps clever starlings can as well. But if there is a genetic component to the behavior -- a reasonable assumption given that starlings form murmurations wherever they are in the world while other birds do not -- then a mechanism for creating the required genetic changes would need to anticipate the need fulfilled by murmurations. Darwinian evolution is blind and unguided, incapable by definition of anticipating anything. In the case of human flight, various types of formation flying were developed in anticipation of a need. Generally that was to survive during battles in the air. Formation flying is not something that pilots stumbled upon in the middle of a dogfight then stuck with; it is a solution to an anticipated need. Intelligence alone has been shown to have produced such solutions.


When it comes to design and murmurations, the elephant in the room is the other abilities birds must possess to achieve the phenomenon. They must have the inclination to fly long distances and to congregate. They must have the ability to navigate, the ability to fly, the ability to perceive and react to the other birds they are flying with, and any number of other wonders. Most people, scientists or not, can see this; but Darwinism demands that we turn a blind eye to such things.

The undeniable logic of the case for design.

File under 'well said' XXXI

Vague and mysterious forms of speech, and abuse of language, have so long passed for mysteries of science; and hard or misapplied words with little or no meaning have, by prescription, such a right to be mistaken for deep learning and height of speculation, that it will not be easy to persuade either those who speak or those who hear them, that they are but the covers of ignorance and hindrance of true knowledge.
John Locke

Demythifying peer review.

For Critics of Intelligent Design, There's No Hiding Behind Claims of "Peer Review" Anymore
David Klinghoffer


Darwinists have had to back off considerably from the once-confident assertion that peer review in science journals constitutes, as Jerry Coyne put it in 2005 inThe New Republic, the "gold standard for modern scientific achievement." The whole institution of peer review is so besmirched now as to arouse, not even amusement anymore, but something more like pity.

In the same article, Coyne maintained that it was precisely by "By that standard" that advocates of the theory of intelligent design "have failed miserably." You mean by the standard of what is now revealed as the intellectual and scientific equivalent of insider trading? Or more like racketeering and simple fraud.

The existence of a blog like  Retraction Watch  is, in this respect, a sign of the times, a measure of the extent to which science publishing has fallen into derision. Their post from a couple of days ago, on a "peer review and citation ring at the Journal of Vibration and Control," has been widely reported, including the retraction of 60 papers from that journal. Sixty!

"This one deserves a 'wow,'" observes author Ivan Oransky. Indeed. The cat is really out of the bag.

Slate:

It may not be entirely fair to liken a "peer review and citation ring" to the academic version of an extortion ring, but there's certainly fraud involved in both. Retraction Watch, a blog dedicated to chronicling which academic papers have been withdrawn, is reporting that SAGE Publishing, a group that puts out numerous peer-reviewed journals, is retracting 60 papers from its Journal of Vibration and Control after an internal investigation uncovered extensive evidence of severe peer-review fraud.

Apparently researcher Peter Chen, formerly of National Pingtung University of Education in Taiwan, made multiple submission and reviewer accounts -- possibly along with other researchers at his institution or elsewhere -- so that he could influence the peer review system. When Chen or someone else from the ring submitted a paper, the group could manipulate who reviewed the research, and on at least one occasion Chen served as his own reviewer.

The Washington Post:

Now comes word of a journal retracting 60 articles at once.

The reason for the mass retraction is mind-blowing: A "peer review and citation ring" was apparently rigging the review process to get articles published.

You've heard of prostitution rings, gambling rings and extortion rings. Now there's a "peer review ring."

The publication is the Journal of Vibration and Control (JVC). It publishes papers with names like "Hydraulic enginge mounts: a survey" and "Reduction of wheel force variations with magnetorheological devices."

The Guardian:

An academic journal has retracted dozens of articles and apologised to readers after falling victim to what it described as a "peer review ring" that appears to have involved more than 100 bogus scholars.

The Journal of Vibration and Control (JVC), a leading publication in the field of acoustics, said it was withdrawing 60 papers published in print and online over the past four years, after discovering that articles were being approved and cited by academics with "assumed and fabricated identities".

The journal's publisher, Sage, said in a statement that the ring appeared to centre around Peter Chen, a researcher formerly of National Pingtung University of Education, in Taiwan. Chen provided an "unsatisfactory response" when confronted, and has since resigned from his post.

Oh, it's just one unfortunate lapse, you say, not representative of anything much beyond itself? If you want to comfort yourself with that idea, first try following the reporting at Retraction Watch, which commonly posts two or three accounts of scholarly fraud and slipshod science per day.

With respect to what this means for the theory of ID, go back and read Casey Luskin's post, "Intelligent Design Is Peer-Reviewed, but Is Peer-Review a Requirement of Good Science" Casey concludes:

Despite the attempted lockout, ID proponents have published their ideas in peer-reviewed scientific journals. This shows that ID has academic legitimacy whether or not one applies the dubious "peer-review" test of good science.

That's right. Going forward, if you want to argue against ID, you are going to have to actually argue against it, critically analyze its arguments and its evidence, as opponents of ID so commonly refuse to do. There's no hiding behind claims of "peer review" anymore.

Miracles for sale.

Darwin of the gaps just so stories re junk DNA becomoing harder to sell

Junk DNA: Is Preventing Breast Cancer a Function?
Evolution News & Views February 6, 2016 4:33 AM 

Each time a function is found for a piece of non-coding DNA, the "junk DNA" myth gets more mythological. Here's a function that has been revealed for a certain long, non-coding transcript of DNA into RNA (lncRNA). It helps prevent breast cancer and ovarian cancer.

Researchers at the University of Bath explain why it is difficult to find these functions for non-coding parts of the genome:

The human genome contains around three metres of DNA, of which only about two per cent contains genes that code for proteins. Since the sequencing of the complete human genome in 2000, scientists have puzzled over the role of the remaining 98 per cent.

In recent years it has become apparent that a lot of this non-coding DNA is actually transcribed into non-coding RNA. However, there is still a debate as to whether non-coding RNA is just 'noise' or whether it serves any function in the cell.

Part of the reason for this uncertainty is that it is very difficult to knock-out non-coding RNA without damaging the DNA, which can lead to off-target effects and false results.

They are clearly aware of the "debate" about junk DNA and the results of ENCODE that found that the majority of the genome is actually transcribed (they referenced ENCODE in the paper). As we have reported often, some members of the evolution side of the debate expect most of the DNA is junk. The design side expects that much of it (but not necessarily all) is functional. Thanks to this research, we have a new case that may point the way to future discoveries.

The news release is titled, "'Junk' DNA plays role in preventing breast cancer." It's based on an open-access paper in Nature Communications. Most readers scanning the paper will see what researchers are up against. Discussion of the complex interactions of parts -- lncRNAs transcripts, small interfering RNAs (siRNAs), promoters, exons, introns, alleles, interference in cis and trans and all the rest -- gets into the technical weeds fast. Thankfully, the release simplifies the essence of the finding. Basically, a piece of non-coding DNA "keeps cells healthy" by preventing a genetic "switch" from getting stuck.

Dr Adele Murrell, from the University of Bath's Department of Biology & Biochemistry, led the study. She explained: "The number of cells in our body are balanced by the level at which cells replicate and replace the ones that die. Sometimes the switches that control this growth get stuck in the 'on' position, which can lead to cancer.

"As the tumour grows and the cancer cells get crowded, they start to break away from the tumour, change shape and are able to burrow through tissues to the bloodstream where they migrate to other parts of the body, which is how the cancer spreads. This process is called metastasis and requires a whole network of genes to regulate the transformation of cell shape and mobilisation.

Dr Lovorka Stojic, from Cancer Research UK Cambridge Institute, the first author of this work identified that GNG12-AS1, a strand of non-coding RNA, prevents the growth switch getting stuck and suppresses metastasis. The specific genomic region where this non-coding RNA is located often gets damaged in breast cancer patients -- this control is removed and the cancer cells spread.

The researchers found that the lncRNA GNG12-AS1 acts as a molecular "rheostat" (their term) that controls the expression of an adjacent gene, DIRAS3, a tumor suppressor. It does it by two mechanisms. One is by regulating the number of transcripts of the tumor suppressor. But if that gets out of control, it can even suppress the "network of genes that prepare cells to change their shape and prepare for metastasis."

By experimentally reducing the amount of GNG12-AS1 produced, either by preventing its transcription or destroying the transcripts, they found that cells start becoming cancerous. This explains why in cancer patients, the switch is stuck:

DIRAS3 is downregulated in 70% of breast and ovarian cancer, and its loss of expression correlates with cancer progression and metastasis. The mechanism responsible for DIRAS3 downregulation to date involves different epigenetic mechanisms and loss of heterozygosity. We hypothesized that TI [transcriptional interference] by GNG12-AS1 could represent an additional layer of regulating DIRAS3 dosage.

The interactions are far more complex than can be described here. Suffice it to say that this long non-coding RNA, which would have been considered "junk" previously, plays a crucial role in regulating the amount of an important tumor suppressor gene. It's a "stable lncRNA localized in the nucleus" with a half-life of 20 to 25 hours, meaning it needs to be transcribed often. Other processes regulate the amount of the lncRNA in a very complex choreography of enhancers, suppressors, and feedback loops. Levels of expression also vary depending on the tissue involved.

It has become increasingly clear that non-coding parts of the genome play vital roles in regulating the coding parts. Regulation is an important function. A system that generates parts without regard to the amount needed is a system out of control. How cool is it to find a code that codes for products that regulate the amount of products in other parts of the code? Not only do we see function emerging for the non-coding regions, we see design on a more colossal scale than anyone could have imagined.

The University of Bath is an internationally recognized center of excellence in biological research. It's encouraging to see their biologists actively challenging the "junk DNA" myth:

Dr Kat Arney, science communication manager at Cancer Research UK, said: "Only a tiny fraction of our DNA contains actual genes, and we know that at least some of the bits in between -- often dismissed as 'junk' -- play important roles in controlling how genes get switched on and off at the right time and in the right place.

When the Human Genome project found that only 2 percent of the genome coded for proteins, the right question should have been, "What is all the rest doing?" Some evolutionists were too quick to dismiss it as a pile of useless leftovers from time and chance. Cancer patients around the world can be grateful that these researchers didn't buy that explanation, but looked beyond the unknown for greater understanding.

"Research like this is helping is to unpick the precise details about how these regions work, shedding light on their potential role in the development [or prevention] of cancer and pointing towards new approaches for tackling the disease."


If a system works, it's not happening by accident. That's the intelligent-design spirit that promises to shed more light into the genomic black box.

21st century divination.

 

The Fragmented Fossil Record of Early Hominins

Casey Luskin

 

 

Despite much hype in the media, the earliest hominin fossils are often so fragmentary that they remain the subject of considerable controversy in the scientific community. Let's examine some of the main early hominin fossils and the debates surrounding them.
Sahelanthropus tchadensis: "Toumai Skull"

Notwithstanding that Sahelanthropus tchadensis (also called the "Toumai skull") is known only from one skull and some jaw fragments, it has been called the oldest known hominin that lies directly on the human line.But not everyone agrees. When the fossil was first reported, Brigitte Senut, a leading researcher at the Natural History Museum in Paris, said "I tend towards thinking this is the skull of a female gorilla."²² Writing in Nature with Milford H. Wolpoff, Martin Pickford, and John Hawks, Senut later noted there are "many... features that link the specimen with chimpanzees, gorillas or both, to the exclusion of hominids," and argued "Sahelanthropus does not appear to have been an obligate biped."²³ In their view, "Sahelanthropus was an ape."²⁴
This debate has continued, but leading paleoanthropologists have cautioned in the Proceedings of the National Academy of Sciences (USA) that teeth and skull fragments alone are insufficient to properly classify or understand species as a hominin: "[O]ur results show that the type of craniodental characters that have hitherto been used in hominin phylogenetics are probably not reliable for reconstructing the phylogenetic relationships of higher primate species and genera, including those among the hominins."²⁵
At one point during the 2009 Texas evolution hearings, anthropology professor Ronald Wetherington testified that "every fossil we find reinforces the sequence that we had previously supposed to exist rather than suggesting something different."²⁶ But this fossil, first reported in 2002, provides a striking counterexample to that assertion. Commenting on the Toumai skull in the journal Nature, Bernard Wood of George Washington University opened by observing, "A single fossil can fundamentally change the way we reconstruct the tree of life."²⁷ He went on to state:

If we accept these as sufficient evidence to classify S. tchadensis as a hominid at the base, or stem, of the modern human clade, then it plays havoc with the tidy model of human origins. Quite simply, a hominid of this age should only just be beginning to show signs of being a hominid. It certainly should not have the face of a hominid less than one-third of its geological age. Also, if it is accepted as a stem hominid, under the tidy model the principle of parsimony dictates that all creatures with more primitive faces (and that is a very long list) would, perforce, have to be excluded from the ancestry of modern humans.²⁸

In other words, if the Toumai skull is accepted as a stem ancestor of humans, then many later supposed human ancestors -- including the acclaimed australopithecines -- ought not be considered human ancestors. Wood concludes that fossils like Sahelanthropus show "compelling evidence that our own origins are as complex and as difficult to trace as those of any other group of organisms."²⁹

Orrorin tugensis: "Orrorin"
Orrorin, which means "original man" in a local Kenyan language, was a chimpanzee-sized primate known only from "an assortment of bone fragments,"³⁰ including pieces of the arm, thigh, and lower jaw, as well as some teeth. When the fossil was initially discovered, the New York Times ran a story titled "Fossils May Be Earliest Human Link,"³¹ and reported it "may be the earliest known ancestor of the human family."³² Despite the meagerness of the find, enough enthusiasm was stirred that an article in Nature soon after the fossil's unveiling cautioned that "excitement needs to be tempered with caution in assessing the claim of a six-million-year-old direct ancestor of modern humans."³³
Some paleoanthropologists claimed that Orrorin's femur indicates a bipedal mode of locomotion that was "appropriate for a population standing at the dawn of the human lineage."³⁴ But as a later Yale University Press commentary admitted, "All in all, there is currently precious little evidence bearing on how Orrorin moved."³⁵
Evolutionary paleoanthropologists often assume that bipedality is a litmus test for membership along the human line. So if Orrorin did prove to be an upright-walking ape-like creature from six million years ago (mya), would that qualify it as a human ancestor? Not at all. In fact, the fossil record contains bipedal apes that evolutionists recognize were far removed from the human line. In 1999, UC San Diego biologist Christopher Wills observed that "[u]pright posture may not be unique to our own lineage" since "[a]n ape that lived ten million years ago on Sardinia, Oreopithecus bambolii, seems to have acquired similar capabilities, perhaps independently."³⁶ A more recent article in Science Daily elaborated:

Oreopithecus bambolii, a fossil ape from Italy shares many similarities with early human ancestors, including features of the skeleton that suggest that it may have been well adapted for walking on two legs. However, the authors observe, enough is known of its anatomy to show that it is a fossil ape that is only distantly related to humans, and that it acquired many "human-like" features in parallel.³⁷

A 2011 paper in Nature by Bernard Wood and Terry Harrison explains the implications of bipedal apes that had nothing to do with human origins:

The object lesson that Oreopithecus provides is critical to the debate about interpreting the relationships of the earliest purported hominins. It demonstrates how features considered to be hominin specializations can be shown to have been acquired independently in a non-hominin lineage in association with inferred behaviors that are functionally related to, but not necessarily narrowly restricted to, terrestrial bipedalism.³⁸

Much as the Toumai skull threatened to displace australopithecines from our ancestral line, Pickford and his co-authors argued that if their hypothesis about Orrorin is correct, then australopithecines are again no longer ancestral to humans, but were merely "a side branch of hominid evolution that went extinct."³⁹ This hypothesis was not well received by many paleoanthropologists, because they need the australopithecines to serve as an evolutionary precursor leading to our genus Homo. Another paper in Nature showed how dissenting views are treated in paleoanthropology, charging that Pickford's "simple phylogeny contrasts starkly with mainstream ideas about human evolution, and glosses over many areas of controversy and uncertainty."⁴⁰

While Orrorin offers evolutionary paleoanthropologists the tantalizing possibility of a bipedal creature that lived around the time of the supposed split between humans and chimpanzees, simply too little of it is known at present to make confident claims about its locomotion, or its proper place in the supposed evolutionary tree.
Ardipithecus ramidus: "Ardi"
In 2009, the journal Science announced the publication of long-awaited reports about a 4.4 mya fossil named Ardipithecus ramidus. Expectations were high as its discoverer, UC Berkeley paleoanthropologist Tim White, had previously promised the fossil was a "phenomenal individual" that would be the "Rosetta stone for understanding bipedalism."⁴¹ When the papers were finally released, the science media took it as an opportunity to evangelize the public for Darwin via the fossil they affectionately dubbed "Ardi."
The Discovery Channel ran the headline "'Ardi,' Oldest Human Ancestor, Unveiled," and quoted White who stated that Ardi is "as close as we have ever come to finding the last common ancestor of chimpanzees and humans."⁴² The Associated Press headline read "World's oldest humanlinked skeleton found," with the article claiming "the new find provides evidence that chimps and humans evolved from some long-ago common ancestor."⁴³
The journal Science named Ardi the "breakthough of the year" for 2009,⁴⁴ and officially introduced her with an article titled "A New Kind of Ancestor: Ardipithecus Unveiled."⁴⁵
Calling this fossil "new" was not quite accurate, since Ardi was discovered in the early 1990s. Why did it take over 15 years for reports to be published? A 2002 article in Science explains that initially the bones were so "soft," "crushed," "squished," and "chalky," that White reported, "when I clean an edge it erodes, so I have to mold every one of the broken pieces to reconstruct it."⁴⁶ Later reports similarly acknowledged that "some portions of Ardi's skeleton were found crushed nearly to smithereens and needed extensive digital reconstruction," and that its pelvis initially "looked like an Irish stew."⁴⁷
The 2009 report in Science tells a striking story of the fossil's poor quality: "[T]he team's excitement was tempered by the skeleton's terrible condition. The bones literally crumbled when touched. White called it road kill. And parts of the skeleton had been trampled and scattered into more than 100 fragments; the skull was crushed to 4 centimeters in height."⁴⁸ In an article titled "Oldest Skeleton of Human Ancestor Found," the science editor at National Geographic put it this way: "After Ardi died, her remains apparently were trampled down into mud by hippos and other passing herbivores. Millions of years later, erosion brought the badly crushed and distorted bones back to the surface. They were so fragile they would turn to dust at a touch."⁴⁹
Claims about bipedal locomotion in hominids require careful and accurate measurements of the precise shape of various bones. How far should one trust claims about Ardi as a "Rosetta stone for understanding bipedalism" when the bones were initially "crushed to smithereens" and "would turn to dust at a touch"? Several skeptical paleoanthropologists felt those claims warranted little credence. As Science reported:

[S]everal researchers aren't so sure about these inferences. Some are skeptical that the crushed pelvis really shows the anatomical details needed to demonstrate bipedality. The pelvis is "suggestive" of bipedality but not conclusive, says paleoanthropologist Carol Ward of the University of Missouri, Columbia. Also, Ar. ramidus "does not appear to have had its knee placed over the ankle, which means that when walking bipedally, it would have had to shift its weight to the side," she says. Paleoanthropologist William Jungers of Stony Brook University in New York State is also not sure that the skeleton was bipedal. "Believe me, it's a unique form of bipedalism," he says. "The postcranium alone would not unequivocally signal hominin status, in my opinion."⁵⁰

A subsequent paper by primatologist Esteban Sarmiento in Science noted that "All of the Ar. ramidus bipedal characters cited also serve the mechanical requisites of quadrupedality, and in the case of Ar. Ramidus foot-segment proportions, find their closest functional analog to those of gorillas, a terrestrial or semiterrestrial quadruped and not a facultative or habitual biped."⁵¹

Critics also questioned the claim that Ardi was necessarily ancestral to humans. When Ardi's reports were first published, Bernard Wood stated, "I think the head is consistent with it being a hominin... but the rest of the body is much more questionable."⁵² Two years later, Wood co-wrote a paper in Nature elaborating on those criticisms, observing that if "Ardipithecus is assumed to be a hominin," and ancestral to humans, then this implies the fossil had "remarkably high levels of homoplasy among extant great apes."⁵³ In other words, Ardi had many ape-like characteristics which, if we set aside the preferences of many evolutionary paleoanthropologists, might imply a much closer relationship to living apes than to humans. According to a Science Daily article reporting on Wood's Nature paper, the claim of Ardi "being a human ancestor is by no means the simplest, or most parsimonious explanation."⁵⁴ Stanford University anthropologist Richard Klein put it this way: "I frankly don't think Ardi was a hominid, or bipedal."⁵⁵
Sarmiento observed that Ardi had characteristics that are different not just from humans, but also from apes. In a Time Magazine interview, "Ardi: The Human Ancestor Who Wasn't?," he elaborated:

"[Tim White] showed no evidence that Ardi is on the human lineage," Sarmiento says. "Those characters that he posited as relating exclusively to humans also exist in apes and ape fossils that we consider not to be in the human lineage."
The biggest mistake White made, according to the paper, was to use outdated characters and concepts to classify Ardi and to fail to identify anatomical clues that would rule her out as a human ancestor. As an example, Sarmiento says that on the base of Ardi's skull, the inside of the jaw joint surface is open as it is in orangutans and gibbons, and not fused to the rest of the skull as it is in humans and African apes -- suggesting that Ardi diverged before this character developed in the common ancestor of humans and apes.⁵⁶

Whatever Ardi may have been, everyone agrees that this fossil was initially badly crushed and needed extensive reconstruction. Its discoverers adamantly maintain the specimen was a bipedal human ancestor, or something very close to it. No doubt this debate will continue, but are we obligated to take for granted the bold talking points promoted by Ardi's discoverers in the media? Sarmiento doesn't think so. According to Time Magazine, he "regards the hype around Ardi to have been overblown."⁵⁷

[Editor's Note: This is an excerpt from Chapter 3, "Human Origins and the Fossil Record," of the new book Science and Human Origins, co-authored by Ann Gauger, Douglas Axe, and Casey Luskin. For details, see Discovery Institute Press.]
References Cited:
[22.] "Skull find sparks controversy," BBC News (July 12, 2002), accessed March 4, 2012, "One of Dr Senut's colleagues, Dr. Martin Pickford, who was in London this week, is also reported to have told peers that he thought the new Chadian skull was from a 'proto-gorilla.'"
[23.] Milford H. Wolpoff, Brigitte Senut, Martin Pickford, and John Hawks, "Sahelanthropus or 'Sahelpithecus'?," Nature, 419 (October 10, 2002): 581-82.
[24.] Ibid.
[25.] Mark Collard and Bernard Wood, "How reliable are human phylogenetic hypotheses?," Proceedings of the National Academy of Sciences (USA) , 97 (April 25, 2000): 5003-06.
[26.] Ronald Wetherington testimony before Texas State Board of Education (January 21, 2009). Time Index 2:06:00-2:06:08.
[27.] Bernard Wood, "Hominid revelations from Chad," Nature, 418 (July 11, 2002):133-35.
[28.] Ibid.[29.] Bernard Wood, "Hominid revelations from Chad," Nature, 418 (July 11, 2002):133-35.
[30.] Potts and Sloan, What Does it Mean to be Human?, 38.
[31.] John Noble Wilford, "Fossils May Be Earliest Human Link," New York Times (July 12, 2001), accessed March 4, 2012, http://www.nytimes.com/2001/07/12/world/fossils-may-be-earliest-human-link.html.
[32.] John Noble Wilford, "On the Trail of a Few More Ancestors," New York Times (April 8, 2001), accessed March 4, 2012, http://www.nytimes.com/2001/04/08/world/on-the-trail-of-a-few-more-ancestors.html.
[33.] Leslie C. Aiello and Mark Collard, "Our newest oldest ancestor?," Nature, 410 (March 29, 2001): 526-27.
[34.] K. Galik, B. Senut, M. Pickford, D. Gommery, J. Treil, A. J. Kuperavage, and R. B. Eckhardt, "External and Internal Morphology of the BAR 1002'00 Orrorin tugenensis Femur," Science, 305 (September 3, 2004): 1450-53.
[35.] Sarmiento, Sawyer, and Milner, The Last Human: A Guide to Twenty-two Species of Extinct Humans, 35.
[36.] Christopher Wills, Children of Prometheus: The Accelerating Pace of Human Evolution (New York: Basic Books, 1999), 156.
[37.] "Fossils May Look Like Human Bones: Biological Anthropologists Question Claims for Human Ancestry," Science Daily (February 16, 2011), accessed March 4, 2012, http://www.sciencedaily.com/releases/2011/02/110216132034.htm.
[38.] Bernard Wood and Terry Harrison, "The evolutionary context of the first hominins," Nature, 470 (February 17, 2011): 347-52.
[39.] Martin Pickford, "Fast Breaking Comments," Essential Science Indicators Special Topics (December 2001), accessed March 4, 2012, http://www.esi-topics.com/fbp/comments/december-01-Martin-Pickford.html.
[40.] Aiello and Collard, "Our newest oldest ancestor?," 526-27.
[41.] Tim White, quoted in Ann Gibbons, "In Search of the First Hominids," Science, 295 (February 15, 2002): 1214-19.
[42.] Jennifer Viegas, "'Ardi,' Oldest Human Ancestor, Unveiled," Discovery News (October 1, 2009), accessed March 4, 2012, http://news.discovery.com/history/ardi-human-ancestor.html.
[43.] Randolph E. Schmid, "World's oldest human-linked skeleton found," MSNBC (October 1, 2009), accessed March 4, 2012, http://www.msnbc.msn.
com/id/33110809/ns/technology_and_science-science/t/worlds-oldest-human-linked-skeleton-found/.
[44.] Ann Gibbons, "Breakthrough of the Year: Ardipithecus ramidus," Science, 326 (December 18, 2009): 1598-99.
[45.] Ann Gibbons, "A New Kind of Ancestor: Ardipithecus Unveiled," 36-40.
[46.] Gibbons, "In Search of the First Hominids," 1214-19.
[47.] Michael D. Lemonick and Andrea Dorfman, "Ardi Is a New Piece for the Evolution Puzzle," Time (October 1, 2009), accessed March 4, 2012, http://www.time.com/time/printout/0,8816,1927289,00.html.
[48.] Gibbons, "A New Kind of Ancestor: Ardipithecus Unveiled," 36-40. See also Gibbons, The First Human: The Race to Discover our Earliest Ancestors, 15 ("The excitement was tempered, however, by the condition of the skeleton. The bone was so soft and crushed that White later described it as road-kill").
[49.] Jamie Shreeve, "Oldest Skeleton of Human Ancestor Found," National Geographic (October 1, 2009), accessed March 4, 2012, http://news.nationalgeographic.com/news/2009/10/091001-oldest-human-skeleton-ardi-missinglink-chimps-ardipithecus-ramidus.html.[50.] Gibbons, "A New Kind of Ancestor: Ardipithecus Unveiled," 36-40.
[51.] Esteban E. Sarmiento, "Comment on the Paleobiology and Classification of Ardipithecus ramidus," Science, 328 (May 28, 2010): 1105b.
[52.] Gibbons, "A New Kind of Ancestor: Ardipithecus Unveiled," 36-40.
[53.] Wood and Harrison, "The evolutionary context of the first hominins," 347-52.
[54.] "Fossils May Look Like Human Bones: Biological Anthropologists Question Claims for Human Ancestry."
[55.] John Noble Wilford, "Scientists Challenge 'Breakthrough' on Fossil Skeleton," New York Times (May 27, 2010), accessed March 4, 2012, http://www.nytimes.com/2010/05/28/science/28fossil.html.
[56.] Eben Harrell, "Ardi: The Human Ancestor Who Wasn't?," Time (May 27, 2010), at http://www.time.com/time/health/article/0,8599,1992115,00.html.
[57.] Ibid.