Piercing the fog?

Disregarding Fake News from Darwin Promoters, South Dakota Scientist Applauds Academic Freedom Bill
Evolution News & Views

Pierre, SD -- This year, South Dakota has an opportunity to encourage more scientific inquiry in the classroom. The state's legislature is considering an academic freedom bill, SB 55, introduced by Senator Jeff Monroe. noted here last week, the bill seeks to thwart censorship, yet ironically is opposed by the National Coalition Against Censorship. The group has misrepresented its contents, comparing mainstream exploration of weaknesses in Darwinian theory with Holocaust denial.

The text of SB 55 says just this:

No teacher may be prohibited from helping students understand, analyze, critique, or review in an objective scientific manner the strengths and weaknesses of scientific information presented in courses being taught which are aligned with the content standards established pursuant to § 13-3-48.

A prominent South Dakota scientist we heard from gets it, applauding the bill as a means to foster critical thinking. "SB 55, under consideration by the South Dakota legislature, is a promising step forward for South Dakota science education," said William S. Harris, PhD. Dr. Harris is the President of OmegaQuant Analytics, LLC (Sioux Falls, SD), and an NIH-funded biomedical researcher with over 300 scientific publications.

Under this legislation, students would have the opportunity learn more about scientific topics, practice critical thinking, and engage with scientific questions facing researchers today. One of those questions pertains to the origin of biodiversity.

Harris commented:

Scientific controversy over the ability of Darwin's version of evolution (i.e., natural selection acting blindly on random mutations) to explain the expanse of life on this planet continues to grow with each new revelation of the exceeding complexity of even the "simplest" life forms, not to mention humans. In my view, it is very important for today's students to understand the evidence for and against important scientific theories like Darwinism and to honestly consider challenges even to such long-held dogmas.

"South Dakota students can only benefit from such an approach -- and hopefully, legislators will seize this occasion to promote scientific inquiry," added Harris. If the bill is enacted, South Dakota would join Louisiana, Tennessee, and at least five other states with science standards or laws recognizing the role of teaching scientific strengths and weaknesses in the classroom.


The law has been a target for activists and journalists spreading misinformation about what SB 55 would permit. We have addressed false claims from Americans United for Separation of Church and State and the Washington Post, which merit being described as fake news,   here and here .

Darwinism v. commonsense

A brief history of the Cuban missile crisis.

Negative to affirmative action on campus?

The fall of Rome II?

Through the looking glass?

South Dakota Science Education Controversy Gets Surreal as Anti-Censorship Group Demands Censorship

David Klinghoffer

We have patiently explained why the current academic freedom bill in South Dakota, SB 55, cannot possibly be construed in any reasonable manner as seeking to inject teaching intelligent design into public schools. As noted yesterday, that didn't stop a prominent lobbying group, Americans United for Separation of Church and State, from working the phrase, "intelligent design," six times into a statement directed against the bill.

One of those instances was in a photo caption of an instructor in front of his class, "Teachers should not be given leeway to introduce intelligent design in science classes."

But with evolution proponents, such distortions are absolutely routine. It's bizarre. It's farcical. But this tops it. In a surreal move, a group called the National Coalition Against Censorship has plunged into the South Dakota situation to demand continued restraints on teachers and their academic freedom -- in other words, censorship.

They complain that SB 55 would "remov[e] accountability in science education." "Accountability" there would seem to mean instructors being vulnerable to career retaliation for teaching critical thinking skills to science students. These "anti-censorship" proponents advocate retaining the option of punishing biology teachers for going off message on Darwinism.

They go on: "Essentially, [the bill] removes the restraints on teachers that prevents them from straying from professionally-developed science standards adopted by state educators." The National Coalition Against Censorship favors keeping "restraints" on teachers firmly in place.

The bill, they say, "may encourage teachers who object to the scientific consensus on evolution and climate change to bring their opinions into the classroom," instead of sticking slavishly to a uniform Darwin-only script. The teachers should stick to their script.

Then there's this. Look again at the  language of the bill. It's very brief:

No teacher may be prohibited from helping students understand, analyze, critique, or review in an objective scientific manner the strengths and weaknesses of scientific information presented in courses being taught which are aligned with the content standards established pursuant to § 13-3-48.

That is another way of saying no teacher may be censored for challenging students with balanced information from objective science sources. Notice that the language concludes by saying that the "strengths and weaknesses" approach may be extended only to "scientific information presented in courses being taught which are aligned with the content standards" already established.

Because intelligent design isn't part of those content standards, the law extends no protection for teaching about ID. Because the content standards are already defined, instruction that's not "aligned" with them, in other words that "stray[s] from professionally-developed science standards adopted by state educators," would also not be protected.

But interestingly, if you read the statement from the "anti-censorship" group, their quotation from the bill cuts off before getting to the part about how instruction must be "aligned with the content standards." The whole proposed law is just a sentence long, but they truncate it a little more than half way through, perhaps to keep the reader from realizing that their dire prediction of teachers "straying" is undercut by the clear language of SB 55 itself. The anti-censorship activists are engaging in censorship right there in the middle of their own statement.

They conclude by comparing exploring mainstream debate about evolutionary theory with, yes, denying the Holocaust. And that is where they transition from absurdity to obscenity.

Good gravy. These complaints, whether from Americans United or from the horrifically misnamed National Coalition Against Censorship, are totally detached from a straightforward reading of the law they wish to attack. They are mere scaremongering, and frankly, contemptible.

In this, though, they're not much worse than supposedly objective news outlets like the Washington Post or ProPublica. When it comes to defending evolutionary orthodoxy, journalism and propaganda merge seamlessly.

Fake news alert (again)

Activist Group Spreads Falsehoods About South Dakota Science Education Bill
Evolution News & Views

Pierre, SD -- Dogmatic activists are trying to derail a proposed science education bill in South Dakota. The language of the bill is aimed at supporting critical thinking by allowing students to learn how scientists debate scientific issues, according to John West, Associate Director of Discovery Institute's Center for Science & Culture.

South Dakota legislators are currently considering SB 55, "An Act to protect the teaching of certain scientific information." Since the bill was introduced, Darwin-only lobbyists with the national group Americans United for Separation of Church and State have been attacking SB 55 and circulating misinformation about it. Notably, they falsely claim that SB 55 would authorize the teaching of "intelligent design."

"Americans United is so worried about what's between the words of the bill, they aren't paying attention to what the words in the bill actually say," said Dr. West in reference to a blog post  this week from the group.

"Contrary to what Americans United says, SB 55 explicitly limits authorization to 'scientific information presented in courses being taught which are aligned with the content standards,'" said Sarah Chaffee, Program Officer in Public Policy and Education at Discovery Institute.

Chaffee points out that South Dakota's current science content standards do not include intelligent design, and thus the bill does not protect the teaching of ID (which is different from creationism). The bill only pertains to topics already in the standards. Yet the post from Americans United mentions intelligent design six times.


"The academic freedom bill does not require teachers to teach anything differently," said Chaffee. "Scientific topics will still be taught as required by state law. But it also gives teachers academic freedom to choose to teach about both "the strengths and weaknesses of scientific information" in the standards -- such as evidence for and against the neo-Darwinian "consensus."

Scientism's brave new world Just keeps getting closer.

Scientists Want to Genetically Engineer Humans

Wesley J. Smith

I first got involved deeply in the debates over biotechnology during the great embryonic stem cell controversy. During that time, I watched in stunned and appalled amazement as scientists lied to legislators and hyped the imminent likelihood of CURES! CURES! CURES! in order to win a political fight and gain federal research grants.

With that experience, I concluded that many in the biotech sector have what amounts to an arrogant "we decide" attitude as to what should and should not be done in science -- rather than society as a whole determining proper parameters through democratic processes -- and moreover, that some have an essentially "anything goes" mentality at odds with the views of the rest of society.

Further, these advocates pretend to be willing to accept reasonable limitations. But a close look reveals these restraints are primarily over things they cannot yet do. Then, after a controversial technology becomes doable, the once "unthinkable" is suddenly moved into the "full speed ahead!" file.

Now, that pattern holds with human genetic engineering. From  From the New York Times story:

An influential science advisory group formed by the National Academy of Sciences and the National Academy of Medicine on Tuesday lent its support to a once unthinkable proposition: the modification of human embryos to create genetic traits that can be passed down to future generations.

This type of human gene editing has long been seen as an ethical minefield. Researchers fear that the techniques used to prevent genetic diseases might also be used to enhance intelligence, for example, or to create people physically suited to particular tasks, like serving as soldiers...

Just over a year ago, an international group of scientists said it would be "irresponsible to proceed" with making heritable changes to the human genome until risks could be better assessed and there was "broad societal consensus about the appropriateness" of any proposed change. No one is pretending that such a consensus now exists.

But in the year that the committee was deliberating, [bioethicist] Ms. [Alta] Charo said, the techniques required to perform this sort of gene editing have passed crucial milestones.

See what I mean?


It starts with health and that justification is deployed to sway the public and regulators. But soon, these technologies will move to promoting enhancement and eugenic design, already seen in currently deployed reproductive technologies. Know this.

Waiting in vain?

Eye Evolution: The Waiting Is the Hardest Part
Brian Miller 

Without calling it a series, I've written several articles recently that followed a logical path. In the first, I described the distinction between   incremental innovation and radical innovation. I also outlined the commonalities and differences between intelligent design and theistic evolution (TE) as approaches to biology. In a follow-up, I applied the concepts from the first article to the  proposed evolution of the vertebrate eye, demonstrating that it could not have occurred without intelligent direction. That's mainly because the majority of steps required for the addition of a lens are disadvantageous in isolation, so selective pressures would have operated in opposition to the evolutionary process.

Let's now consider the challenge of waiting times -- the minimum time required for hypothesized evolutionary transformations, such as the development of the camera eye, to occur through undirected processes. Even if the selective pressures were favorable, the required timescales are far longer for sufficient numbers of coordinated mutations to accumulate than the maximum time available, as determined by the fossil record. Of special interest is the proposed cooption of crystallin proteins, which give the lens its refractive properties. Seemingly, one of the easiest evolutionary steps should be producing these proteins in the lens, for some of them are already used for other purposes. The main hurdle would simply be altering the regulatory regions of the first borrowed crystallin gene and other related genes, so they bind to the correct set of transcription factors (TFs). The lens protein could then be overexpressed in the fiber cells in sufficient quantities at the right time in development.

However, the cooption process is far more challenging than it might at first appear. It requires specific regulatory regions to bind to well over four new transcription factors. This alteration would involve numerous mutations creating over four corresponding DNA binding sites known as transcription factor binding sites (TFBS). As I mentioned in the previous article, the earliest lens should have closely resembled lenses of vertebrates today, so this lower estimate is almost certainly accurate.

A typical binding site involved in lens construction consists of a DNA sequence ranging from roughly 6 (e.g., SOX2) to 15 (e.g., Pax6) base pairs, so four TFBS would likely correspond to over 30 base pairs. One could think of these DNA sequences like the launch codes to a missile; they must be correct before the protein can be properly manufactured. The lower bound of 30 base pairs can be divided by a factor of 3 to compensate for sequence redundancies, flexibility in where in the DNA sequences start, and the fact that roughly one quarter of the bases would be correct purely by chance. This extremely conservative estimate indicates that over 10 mutations would be required to generate a proper sequence. All but the final mutation would be neutral.

We can now calculate the likelihood of sufficient mutations occurring in 10 million generations. The mutation rate for a specific base par is typically estimated for complex animals to correspond to a probability around 1 in 100 million. The chance of a mutation occurring in 10 million generations is then 1 in 10. Therefore, the chance of 10 coordinated mutations appearing on the same DNA strand works out to much less than 1 in 10 billion. No potential precursor to a vertebrate with a lens would have had an effective population large enough to acquire the needed mutations. For comparison, the effective population size estimate used for Drosophila melanogaster can be in the low millions. If the generation time were even as low as one year, a crystallin could not be coopted even in 10 million years, which is the time required for the appearance of most known phyla in the Cambrian explosion.

Moreover, this step is only one of hundreds required to produce a lens. Researchers have identified numerous TFs essential to lens development in vertebrates, and each has its own set of TFBS, which integrate into a complex developmental regulatory gene network. If only one connection were wired incorrectly, the eye in the vast majority of cases would not form properly, resulting in impaired vision. In addition, the lens is only one component of the eye, which is only one part of the visual system. The obvious conclusion is that, in the timeframe allowed by the fossil record, the reengineering to produce the vertebrate visual system would require foresight and deliberate coordination. Those are the hallmarks of design.

Biologists have claimed to produce viable scenarios for the evolution of several other complex systems. What all these stories share is that they ignore crucial details and lack careful analysis of feasibility. When we examine these issues in detail, the stories collapse for the same reasons that the one about the eye does: First, the selective pressures oppose transitions between key proposed stages. Second, the required timescales are vastly longer than what is available.

For biologists, rigorously evaluating evolutionary narratives has become fully possible only in the past several decades due to advances in molecular and developmental biology. Meanwhile, with breakthroughs in computer engineering, information theory, and nanotechnology, parallels between biological and human engineered systems are increasingly evident. These developments are making the intelligent design framework essential for scientific advancement. They also create new opportunities for ID proponents and theistic evolutionists to collaborate.

Proponents of TE want to push materialistic explanations for biological systems as far as possible, as science demands. ID advocates would not disagree with them on that. No one wants to trigger the design filter prematurely. So theistic evolutionists should join us in considering what the modern evolutionary synthesis with its auxiliary hypotheses, such as niche construction and epigenetic inheritance, can explain. We should all continue to examine how insights from evolution may benefit research on cancer, in epidemiology, and other fields.

ID researchers, meanwhile, can examine the limits of purely materialistic processes, and we invite theistic evolutionists to do likewise These combined efforts will help to define in greater detail what Michael Behe calls the edge of evolution. This understanding would also help advance research on cancer treatments, antibiotic protocols, and more. At the same time, ID proponents can help identify how principles and insights from engineering may advance biological research and related applications.

Many theistic evolutionists recognize that the appearance of design is real (but then, so does Richard Dawkins). This insight, at least, should inform their research. In contrast, anti-theistic evolutionists are biased against recognizing the benefits of design thinking. As a result, in studying life they have stumbled upon close parallels to human engineering, which, however, they recognized only begrudgingly. On the other hand, ID expects these parallel and is unsurprised to find them. A classic example is how researchers, misled by evolutionary thinking, dismissed a large portion of the human genome as "junk" DNA instead of anticipating that it would function as a  genomic operating system.


TE researchers do not need to immediately agree with ID researchers on whether any particular feature of life is the result of primary design or secondary causes. They can still work together to best serve the cause of genuine science, and I hope they will do so more in the future.

The fine print.

What Darwinists Don't Tell You: Valentine's Day Edition
David Klinghoffer

Darwinism is replete with salesmanship, some of it thoroughly deceptive. Pushing the false dichotomy of evolution versus Young Earth Creationism, as if there were no alternative to these two, is one way that evolutionists bully and mislead non-scientists. Sadly, they are joined in this by some creationists.

Tom Bethell, author of  Darwin's House of Cards: A Journalist's Odyssey Through the Darwin Debates, points out that from Darwin himself on up to today, advocates of the theory have habitually  played down the conflict between their materialism, on one hand, and religious belief on the other.

One doesn't hear much about the materialism of Darwin and Darwinism, likely because there has been a longstanding effort to ignore and suppress it. Many of today's theistic Darwinists play this game, but they are hardly the first.
Similarly, only the most perilously candid evolutionists are in your face about another straightforward inference from materialism: the denial of free will. Bethell again:

The materialist philosophy puts its advocates at odds with the great majority of mankind, alerting the rest of us to the implausibility of what we are expected to believe. Being told that "evolution is a fact" can be intimidating because many laymen won't know how to respond. But to be told, "Your will is not free, even though you think it is," or "You're an automaton and you don't even know it," is likely to get people's backs up.
This bleak vision, the human being as meat machine, is on vivid display, though mixed with a clumsy childlike enthusiasm, in the writing of emeritus University of Chicago evolutionary biologist Jerry Coyne. On Darwin Day, for instance, he chided me for the hope that evidence of design will overcome Darwinian censorship: "I'm sorry to say that, I think, Klinghoffer will go to his Maker (disassociated molecules) before a teleological view of life permeates evolutionary biology."

Imagine trying to sell "disassociated molecules" to the public, with their human intuitions, fears, and longings. Darwinists like Coyne or Dawkins, Bethell observes, are their own worst enemies.

To these thoughts, add our colleague Jonathan Witt's observation for Valentine's Day over at The Stream. From Darwinian materialism, he notes, a denial of the reality of love must follow:

Evolutionist Daniel Dennett  called  Darwinism a "universal acid" that "eats through just about every traditional concept ... dissolving the illusion of our own authorship, our own divine spark of creativity and understanding."
Dissolve those things and there's no room for romantic love to be anything very exalted.

Biologist E.O. Wilson is   just as blunt. When Darwinian science conquers all, we will view the human brain as just the "product of genetic evolution by natural selection." And the mind "will be more precisely explained as an epiphenomenon of the neuronal machinery of the brain."

But surely we can rescue things like art, religion and poetry, right? No, Wilson insists. Evolution teaches us that all of it was "produced by the genetic evolution of our nervous and sensory tissues."

Evolving Away Love

So what becomes of Valentine's Day, of all of those romantic longings and pledges to love, honor and protect, maybe even till death do us part? Yes, glands and instincts are involved. Only a gnostic would deny that, and Christianity threw Gnosticism out on its ear at the Incarnation and the Resurrection.

But Darwinian science goes further. It insists the stuff of Valentine's Day is all glands and instincts, and beneath those, all brain chemistry -- a soulless concoction of matter and energy stirred up in the alchemist's lab we call evolution.

Of course, it would have to be that way. A materialist understanding of evolution robs us of virtually everything that makes life rich and worth living, if we're honest about it with ourselves. What, really, is left? Eating? Animal rutting? Pursuing status or dominance in a manner hardly different from the way chimps and chickens do?

But Darwinists, devoted salesmen that they are, often seem freaked out about the implications of their theory, and so try to take those back, sometimes in the space between one paragraph and the next. Dennett, for one, preaches the illusion of consciousness. But just as we know that love is real and not only a matter of glands in action, and as we know that are our will is ultimately free, we also have a strong sense that our inner lives are genuine.

So here is neuroscientist Michael Gazzaniga giving a reverent review to Dennett's new book, From  From Bacteria to Bach and Back: The Evolution of Minds, in the Wall Street Journal  and getting tangled up in the consciousness question. On one hand, says Gazzaniga:

[Dennett's] early writings insisted on the idea that consciousness was an illusion, a trick that the multifaceted brain pulled to give us that cozy feeling of an interior experience, with all its fullness -- the redness of red, the painfulness of pain, the euphoria of love.
But most Wall Street Journal readers are going to have a hard time with the idea of their "interior experience" as a trick their brain pulls on them. The notion is thus walked back by Dr. Gazzaniga in the very next paragraph:

This suggestion is quite profound and complicated and has often been misunderstood. In response to Mr. Dennett's early landmark book, "Consciousness Explained" (1991), the cognitive-science cognoscenti quipped that the title should have been "Consciousness Explained Away." That was obviously not Mr. Dennett's point. It was thought by many distinguished philosophers, such as John Searle and Thomas Nagel, that Mr. Dennett was abandoning the first-person experience of consciousness, the personal nature of it, the qualia. He wasn't at all. He never doubted consciousness itself.
Consciousness for Dennett is "an illusion," yet "He never doubted consciousness itself." He never doubted an illusion? I haven't read the book, but the review of it makes no sense.

Darwinism asks us to doubt, to deny, our own intuitions and experiences. Intelligent design cheerfully affirms them. The former, says Jonathan Witt, overwhelms resistance "by endlessly recycling evidence long discredited even by scientists in [Darwinists'] own ranks" (referring to the "icons of evolution" made famous by Jonathan Wells).


Meanwhile, intelligent design is not permitted to make its own scientific case. Or when it does so, ID scientists are put down by censors  or drowned out by media spokesmen with endless chants of "creationist, creationist, creationist." What a mad world!

A trump administration may not mean The end of the republic?:Pros and cons.

The Bard and the art of insult.

On Kafka and the kafkaesque.

Taking an axe to Darwinism's tree of life

When genome mapper Craig Venter made clear he doubted universal common descent…
Posted by News under Evolution, Genomics, Origin Of Life, Tree of life

We’d heard about  Craig Venter’s dissent  before but you should read the whole story: From  Tom Bethell  in  Darwin’s House of Cards: A Journalist’s Odyssey Through the Darwin Debates,

This was publicized in a science forum held at Arizona State University in February 2011, a little over a year after Dawkins’s Greatest Show

was published. The physicist Paul Davies and others, including two Nobel Prize winners, participated in the event, which was videotaped. Richard Dawkins himself was on the panel. The forum addressed the question, “What is life?”Most of the panelists accepted that all organisms on Earth represent a single kind of life because they believed that the genetic code is universal. The NASA scientist and panelist Chris McKay made the case that this single form of life—a “sample of one”—should encourage us to further explore Mars and other planets for signs of life.

Craig Venter then disputed the premise. He challenged the claim “that there’s only one life form on this planet.” We have “a lot of different types of metabolism, different organisms,” he said. He turned to Paul Davies and added: “I wouldn’t call you the same life form as the one we have that lives in pH 12 base. That would dissolve your skin if we dropped you in it.” (pp. 53–54)

Venter went on to doubt that there is a single “tree of life” and evolutionary bioinformatics specialist W. Ford Doolittle noted that “the history of life cannot properly be represented as a tree.”

Guy to watch. In a world where so many people are defending themselves from shadows and rumours, he wants to look at reality. He should be banished from pop science coverage as a bad influence.

What if it turns out that there are multiple streams of life arising from a single era? How would that change the picture of the origin of life?

Undeniably designed.

A Son Realizes the Irrepressible Truth
Howard Glicksman

Recently while seeing a new hospice patient with severe heart failure, I encountered the man's son, who happens to work in manufacturing. The younger man sought to better understand his father's medical condition and with it the relevant treatment options. So, beginning with the anatomy of the heart and its role within the cardiovascular system, we quickly moved on to what happens when the heart fails and how this had manifested in his father.

The son proved to be an astute interlocutor, as each answer engendered another probing question. Soon I had to explain how water is either inside or outside the cell, and if outside, either in the circulation or around the cells. We discussed the effects of hydrostatic and osmotic pressure on water movement in and out of the capillary. In the midst of this, as he gazed away rapt in thought, I assumed he was now content with what I had explained. But then a quizzical look came over his face and he asked, "But what happens to the water that doesn't make it back to the veins?"

I responded, "Ah, have you ever heard of the lymphatics?" and went on to describe this microscopic drainage system. He quickly smiled, tapped the heel of his palm to his forehead, gave out a yell, and exclaimed "What a beautiful design!" As I mentioned, he works in manufacturing and so knows a thing or two about design.

I had just witnessed in action what Douglas Axe describes in his book Undeniable  as the design intuition. It was much more than just an intellectual assent to the truth. It animated the son's whole body as he expressed with joy, despite the painful circumstances of his father's health, the recognition of his own body's design.


It was a natural human response to the facts set before him. Yet in the wake of yesterday's marking of Darwin Day, aka Academic Freedom Day, it's sobering to consider that if he had done this in many a public or private university setting, he likely would have been belittled, criticized, or depending on his position, censured.

No way back for Junk DNA?

With Fresh Funding, ENCODE Team Continues Demolition of "Junk DNA" Myth
Evolution News & Views


Is there treasure in the DNA's so-called "junk" pile? Well, as the first half of a popular saying goes, money talks. The National Institutes of Health (NIH) just funded five centers to explore what the "dark matter genome" (the non-protein-coding part) is doing. Two of the centers will be at the University of California, San Francisco, which describes the new project:

"The Human Genome Project mapped the letters of the human genome, but it didn't tell us anything about the grammar: where the punctuation is, where the starts and ends are," said NIH Program Director Elise Feingold, PhD. "That's what ENCODE is trying to do." [Emphasis added.]
Grammar -- there's an ID-friendly analogy for you. Language students and their teachers don't look for grammar and punctuation in gibberish. The statement implies purpose: functional information that has a beginning and end. Rules that organize information for communication. Genes without grammar are like words without sentences.

Launched in 2003 after the Human Genome Project found that only 2 percent of DNA codes for proteins, ENCODE was tasked "to find all the functional regions of the human genome, whether they form genes or not." Initial results were spectacular, showing that at least 80 percent of DNA is transcribed. This made the #1 spot in our top ten evolution-related stories for 2012 an "easy pick," as Casey Luskin wrote at the time, since it "buries" the "junk DNA" dogma -- the idea that evolution left our genome littered with useless leftovers of mutation and natural selection.

Darwinians don't give up easily, though, as we have often noted. Transcription is not proof of function, they argue. But why use costly resources to transcribe junk for no purpose? In the intervening years, more and more functions have come to light.

The initiative revealed that millions of these noncoding letter sequences perform essential regulatory actions, like turning genes on or off in different types of cells. However, while scientists have established that these regulatory sequences have important functions, they do not know what function each sequence performs, nor do they know which gene each one affects. That is because the sequences are often located far from their target genes -- in some cases millions of letters away. What's more, many of the sequences have different effects in different types of cells.
The new grants from NHGRI [National Human Genome Research Institute] will allow the five new centers to work to define the functions and gene targets of these regulatory sequences.

We anticipate future spectacular discoveries will continue to come from ENCODE. And now researchers have new lights to shine: including faster DNA barcoding and the CRISPR-Cas9 gene-editing tool.

The project's aim is for scientists to use the latest technology, such as genome editing, to gain insights into human biology that could one day lead to treatments for complex genetic diseases.
In addition to the two centers at UCSF, others will be set up at labs including Cornell, Stanford, and Lawrence Berkeley. The National Center for Human Genome Research explains the goals, in which it will invest an initial outlay of $31.5 million for 2017:

At its core, ENCODE is about enabling the scientific community to make discoveries by using basic science approaches to understand genomes at the most fundamental level. Its catalog of genomic information can be used for a variety of research projects -- for example, generating hypotheses about what goes wrong in specific diseases or understanding the processes that determine how the same genome sequence is used in different parts of the body to make cells with specialized functions. More than 1,600 scientific publications by the research community have used ENCODE data or tools.
Other Junk-Busting Research

Meanwhile, labs all over are finding treasure in the formerly dismissed junk. It has become something of a scientific sport these days to get the function ball downfield ahead of other labs.

Enhancer RNAs. Last month, Penn Medicine News threw this touchdown, "'Mysterious' Non-protein-coding RNAs Play Important Roles in Gene Expression." Realizing that transcribing junk didn't make sense, researchers at the University of Pennsylvania suspected that there must be more going on. They asked, Why do body cells turn out so different when they all have the same genome? Seeking function, they learned about the role of enhancer RNAs that regulate which genes get expressed in different types of cells.

DNA repeats. It looks so boring, repetitive DNA. It must be unimportant, right? Not so, found two researchers from Rockefeller University. Writing in PNAS, they discovered that three proteins carefully protect those repeats around centromeres -- the locations on chromosomes where the spindle attaches during cell division. "Our study reveals the existence of a centromere-specific mechanism to organize the repetitive structure and prevent human centromeres from suffering illegitimate rearrangements." Some could lead to cancer and aging. Doesn't the converse, legitimate arrangements, imply complex specified information?

Disordered proteins. Most proteins fold into compact shapes. What are disordered proteins doing, flailing like air dancers in the wind? Canadian researchers publishing in PNAS found one that has a signaling function. It's not alone; intrinsically disordered regions (IDRs) are "widespread" and have "diverse functions," they say. Since they are maintained by "stabilizing selection," they must be doing something important. Oddly, the function remains the same even when the underlying amino acid sequence changes. In one instance in yeast, they found evidence for "selection maintaining this quantitative molecular trait despite underlying genotypic divergence." This could be a major paradigm change, since 40 percent of proteins are predicted to contain "disordered" regions. The one they studied appears to have a signaling function. Now, the hunt is on to find other functions in "disorder" (synonymous with junk).

Accordion genomes. Protein-making is not the only function of DNA. Some of it, we know, provides structural support or anchor points. Researchers at the University of Utah are exploring another mystery: why genomes grow and shrink. By studying the genomes of birds and mammals (including flying mammals, the bats), they speculate that shedding DNA can streamline a bird or bat for flight, but allow other creatures to grow their supply. The stretching and squeezing of genomes they liken to an accordion mechanism. It would seem that extra scaffolding could be jettisoned without harm. Whatever is going on, it doesn't match the old dogmas of neo-Darwinism. "Evolution is often thought of as a gradual remodeling of the genome, the genetic blueprints for building an organism," this article begins. "In some instances it might be more appropriate to call it an overhaul." Since overhauling a genome non-gradually would likely be catastrophic, we suspect scientists will find this process is under careful regulation. "I didn't expect this at all," the lead author remarked. "The dynamic nature of these genomes had remained hidden because of the remarkable balance between gain and loss." Watch this space.


The research strategy of looking for function continues to prove fruitful. It's an attitude that says, If it's there, it's probably doing something important. True, just because some things are designed doesn't imply that everything is designed. But science was hindered for decades by the junk-DNA myth and the vestigial-organs myth, which we now know are being discarded. Science is playing catch-up after years of lazy thinking that reasoned, If it's not doing something I understand right now, it must be junk. It's time now to assume function, until the case is shown to be otherwise. As Paul Nelson says, "If something works, it's not happening by accident."

Darwinism's bridge to nowhere?

Eye Evolution: A Closer Look
Brian Miller

In a  previous article  I described how theories of innovation provide insight into the limits of natural selection. I will now apply those concepts to hypotheses regarding the evolution of the vertebrate eye, a subject that, since the time of Charles Darwin, has been near center of the debate over the creative power of natural selection. As Darwin himself stated in the Origin of Species:

To suppose that the eye with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest degree.
He did, however, still believe it could evolve over numerous gradual increments.

Today, evolutionists propose several of the stages in what they believe to be a plausible evolutionary path. Science writer Carl Zimmer outlined the standard story:

In 2007, Trevor Lamb and his colleagues at Australian National University synthesized these studies and many others to produce a detailed hypothesis about the evolution of the vertebrate eye. The forerunners of vertebrates produced light-sensitive eyespots on their brains that were packed with photoreceptors carrying c-opsins. These light-sensitive regions ballooned out to either side of the head, and later evolved an inward folding to form a cup. Early vertebrates could then do more than merely detect light: they could get clues about where the light was coming from...a thin patch of tissue evolved on the surface of the eye. Light could pass through the patch, and crystallins were recruited into it, leading to the evolution of a lens. At first the lens probably only focused light crudely...Mutations that improved the focusing power of the lens were favored by natural selection, leading to the evolution of a spherical eye that could produce a crisp image.
See Wikipedia for a chart illustrating  "Major stages in the evolution of the eye."

To add weight to this narrative, two biologists created a  computer simulation, demonstrating, in their view, the incremental evolution of an eye in fewer than 400,000 generations.

This often-repeated tale sounds impressive at first, but it is not unlike most supposed explanations of the evolution of complex features. It scores high on imagination and flare but low on empirical evidence and thoughtful analysis. It most certainly does not represent a "detailed hypothesis." Likewise, the simulation does an admirable job of describing how a mechanical eye could develop incrementally, but it is completely disconnected from biological reality. In particular, it ignores the details of how a real eye functions and how it forms developmentally. When these issues are examined, the story completely collapses.

To fully appreciate why that is so requires a basic understanding of developmental biology. During development, cells divide, migrate, and differentiate into a wide variety of types. Throughout this process, the cells send chemical signals to their neighbors, and these signals cause proteins known as transcription factors (TF) to bind to genes in regulatory regions, which control the corresponding genes' activity. The TFs bind to what are called transcription factor binding sites (TFBS), and the correct binding enables the genes to produce their proteins in the right cells at the right time in the right amount.

The evolution of additional components in the vertebrate eye requires that this network of intercellular signals, TFs, TFBS, chromatin remodeling, as well as many other details be dramatically altered, so that each developmental stage can progress correctly. For instance, the seemingly simple addition of a marginally focusing lens -- that is to say, a lens that directs slightly more light onto a retina -- requires a  host of alterations:

Ectodermic tissue folds into a lens placode, which then forms a lens vesicle.

Cells in the lens vesicle differentiate into lens fibers, which elongate to produce the proper lens shape.

The lens fibers then undergo several key modifications, including tightly binding together, filling almost entirely with special refractive proteins called crystallins, developing special channels to receive nutrients, and destroying their organelles.

All of these steps must proceed with great precision to ensure the end product focuses light in an improved manner. The development of the lens in  all vertebrates  is very similar, and it even resembles that in  other phyla. Therefore, the development of the first lens should have closely followed the steps outlined above with only minor differences, inconsequential to the basic argument.

The challenge to evolution is that, short of completion, most of these changes are disadvantageous. A lens that has not fully evolved through the third step noted above would either scatter light away from the retina or completely block it. Any initial mutations would then be lost, and the process would have to start again from scratch. In the context of fitness terrains, an organism lacking a lens resides near the top of a local peak. The steps required to gain a functional lens correspond to traveling downhill, crossing a vast canyon of visually impaired or blind intermediates, until eventually climbing back up a new peak corresponding to lens-enhanced vision.

Once an organism has a functional lens, natural selection could then potentially make gradual improvements. However, moving from a reasonably functional lens to one that produces a high-resolution image is rather complex. In particular, the refractive index (i.e., crystalline concentration) has to be adjusted throughout the lens to vary according to a precise mathematical relationship. A gradual decrease from the inside to the outside is  needed to prevent spherical aberrations blurring the image.

Even more steps are required for the improved image to be properly interpreted:

Feedback circuitry must be added to allow the lens to automatically refocus  on images at different distances.

The retina has to be completely reengineered to process high-resolution images, including the  addition of circuits  to enable edge and motion detection.

The neural networks in the brain have to be rewired to properly interpret the pre-processed high-resolution images  from the retina.

Higher-level brain functions must be enabled to identify different objects, i.e., dangerous ones such as a shark, and properly respond to them.

Until steps 2 through 4 are completed, a high-resolution image would likely prove disadvantageous, since most of the light would be focused on fewer photoreceptors. In insolation, the alterations of perfecting the lens and those involved in step 1 would hinder the analysis of large-scale changes to the field of view, such as identifying the shadow of a predator. Natural selection would thus remove most of the initial mutations, and evolution of the eye would come to a halt.

The difference between blurry and high-resolution vision is well illustrated by the box jellyfish. It has several eyes around its body. Two have lenses, which can produce highly focused images. However, the focal point is past the retina, so the retinal images are blurry. An ability to focus more clearly than is actually useful seems to be an example of gratuitous design. Zoologist Dan Nilsson comments:

For such a minute eye it is surprising to find well-corrected, aberration-free imaging, otherwise known only from the much larger eyes of vertebrates and cephalopods. The gradient in the upper-eye lenses comes very close to the ideal solution...The sharp image falls well below the retina and it would seem that the sharp focus of the lenses is wasted by inappropriate eye geometry.
However, for the box jellyfish a high-resolution image would be disadvantageous, since its neurology is engineered to respond to such bulky features as the edge of a mangrove. Is this blurry vision the result of the jellyfish not having yet evolved high-resolution vision? No: its neural organization is radically different from that needed for the latter. As Nilsson comments, "Another, more likely, interpretation is that the eyes are 'purposely' under-focused."


"Purposeful"? Yes, it would seem so. The example illustrates that low-resolution vision is not at an inferior point on the same fitness peak as high-resolution vision. Instead, both systems reside near the peaks of separate mountains. For any species, upgrading to high-resolution vision requires massive reengineering in a single step. Such radical innovation, coordinated to achieve a distant goal, is only possible with intelligent design.

Yet another ancient witness speaks in the defense of the Bible.: The Watchtower Society's commentary.

Another Bit of Evidence

Is there archaeological evidence supporting the Bible record? In 2014 an article in the magazine Biblical Archaeology Review addressed the question: “How many people in the Hebrew Bible have been confirmed archaeologically?” The answer given: “At least 50!” One man who did not make the list in that article was Tattenai. Who was he? Let us review his brief role in the Bible record.

Jerusalem was once part of a vast Persian Empire. The city lay in an area that the Persians called Across-the-River, that is, to the west of the Euphrates. After conquering Babylonia, the Persians released Jewish captives and authorized them to rebuild Jehovah’s temple in Jerusalem. (Ezra 1:1-4) Enemies of the Jews, however, opposed the project and used it as a pretext to accuse the Jews of rebelling against Persia. (Ezra 4:4-16) During the reign of Darius I (522-486 B.C.E.), a Persian official named Tattenai led an inquiry into the matter. The Bible calls him “the governor of the region Beyond the River.”—Ezra 5:3-7.

A number of cuneiform tablets bearing the name Tattenai have survived as part of what may have been a family archive. The tablet that links one member of this family to the Bible character is a promissory note dated to the 20th year of Darius I, 502 B.C.E. It identifies a witness to the transaction as a servant of “Tattannu, governor of Across-the-River”—the same Tattenai who appears in the Bible book of Ezra.

What was this man’s role? In 535 B.C.E., Cyrus the Great reorganized his dominions into provinces, one of which was called Babylon and Across-the-River. The province was later split into two parts, one of which was simply called Across-the-River. It included Coele-Syria, Phoenicia, Samaria, and Judah and was likely ruled from Damascus. Tattenai governed this region from about 520 to 502 B.C.E.

After traveling to Jerusalem to investigate the accusation of rebellion, Tattenai reported to Darius that the Jews claimed to have received authorization from Cyrus to rebuild Jehovah’s temple. Investigations in the royal archives substantiated that claim. (Ezra 5:6, 7, 11-13; 6:1-3) So Tattenai was ordered not to interfere, and he obeyed.—Ezra 6:6, 7, 13.


To be sure, “Tattenai the governor of the region Beyond the River” merits only a footnote in history. Note, though, that the Scriptures mention him and apply to him exactly the right title. That fact gives us yet another bit of evidence that archaeology repeatedly supports the Bible’s historical accuracy.