It's official, 'Junk DNA'= Junk science

Genetics Leaves Central Dogma and Junk DNA in the Rear-View Mirror
Evolution News | @DiscoveryCSC

Today, we look at some discoveries that continue to leave the Central Dogma and “junk DNA” in the rear-view mirror. Through the front windshield, we see discoveries about epigenetics coming fast.

New Form of Regulatory DNA

A “mysterious” form of DNA shaped like a four-stranded knot, once thought to exist only in the lab, has been discovered to be active in cell nuclei. Yasemin Saplakoglu reports in Live Science that “many scientists thought that it couldn’t possibly exist in human cells,” because it loves acidic environment not found naturally in the body. Called an i-motif, the structure has been now reported by Australian scientists in a paper in Nature Chemistry, and the rush is on to see what it does. Saplakoglu thinks “it may play an important role in regulating our genes.” Co-author Marcel Dinger sees much more to discover in the forward view:

“There’s so much of the genome that we don’t understand, probably like 99 percent of it,” Dinger said. Seeing DNA folded like this in living cells “makes it possible to decode those parts of the genome and understand what they do.”

How often have we heard about new roles for junk DNA? Here’s another: “A conserved function for pericentromeric satellite DNA” announced in the journal eLife by researchers at the University of Michigan. This one got promoted from junk to captain:

A universal and unquestioned characteristic of eukaryotic cells is that the genome is divided into multiple chromosomes and encapsulated in a single nucleus. However, the underlying mechanism to ensure such a configuration is unknown. Here we provide evidence that pericentromeric satellite DNA, which is often regarded as junk, is a critical constituent of the chromosome, allowing the packaging of all chromosomes into a single nucleus.

Old-school geneticists considered this kind of DNA as “junk” or “selfish” DNA that perpetuated itself for no purpose, says Science Daily. But lead author Yukiko Yamashita and colleagues “were not quite convinced by the idea that this is just genomic junk.” For one thing, it is highly conserved, so “If we don’t actively need it, and if not having it would give us an advantage, then evolution probably would have gotten rid of it. But that hasn’t happened.” When they took a closer look, they found that cells in fruit flies, mice, humans and probably all vertebrates cannot survive without it. Using a protein named D1 that binds to the satellite DNA, they found it provides vital attachment points for molecular machines that keep chromosomes in the nucleus. Without it, DNA would float off into buds with only part of the genome, and the cell would die.

The similar findings from both fruit fly and mouse cells lead Yamashita and her colleagues to believe that satellite DNA is essential for cellular survival, not just in model organisms, but across species that embed DNA into the nucleus — including humans.

Genetics Without the “Epi” Prefix Is Incomplete

A geneticist at , Johns Hopkins is telling colleagues not to forget the “epi” in genetics research. “In a review article published April 5 in the New England Journal of Medicine scientist Andrew Feinberg, M.D., calls for more integration between two fields of DNA-based research: genetics and epigenetics.” It is essential for human disease prevention and mitigation, Feinberg notes, but from his vantage point, “scientists know comparatively little about how existing drugs may be altering patients’ epigenomes.” 

He suggests that combining genomewide and epigenomewide association studies can overcome problems of assigning cause and effect to specific alterations among either type of study alone.

Identity Crisis Solved

Why do cells with identical genes perform unique jobs? Consider how different a blood cell is from a brain cell, and yet they both share the same genome in their nuclei. Researchers at Trinity College Dublin explored the question of “cellular identity,” which they say is “central to the field of epigenetics,” and “made a significant discovery that explains how and why the billions of different cells in our bodies look and act so differently despite containing identical genes.”

Central to this is a group of epigenetic regulators, called Polycombs, which are vital to regulating cellular identity in multicellular organisms of both the plant and animal kingdoms. The Bracken lab studies the biology of these Polycomb epigenetic regulators, and their newly discovered PALI1 and PALI2 proteins form a new family of Polycombs that are unique in that they are only present in vertebrates — they are not found in invertebrate animals, or plants.

The uniqueness of these regulators to vertebrate animals does not mean that plants and invertebrates lack mechanisms to achieve cellular identity; they just have different ones.

The Anti-Dogmatists

Confidence in the Central Dogma been collapsing for a long time now. The idea that DNA is the master molecule, making RNA that makes proteins and that’s all you need to know — taught uncritically since the 1960s — cannot stand up to all the new discoveries. At The Conversation, Staffan Müller-Wille and Hans-Jörg Rheinberger explain “Why genes don’t hold all the answers for biologists.”

It is still widely believed that the gene is the foundation of life — that its discovery has provided information about how all living beings are controlled by the genetic factors they inherit from their parents.

But scientists and philosophers are beginning to doubt the relevance of the gene for understanding biology.

Despite being central to the subject for over a century, there has never been a universally accepted, constant definition of what genes actually are. From the beginning, scientists have tried to link human characteristics to genes, but had limited success in establishing stable connections.

Rheinberger is a historian of science at the Max Planck Institute. Together, the two produced a book called The Gene: From Genetics to Postgenomics that undermines the neat picture of genetics as a triumph of 20th-century science. While readers of the press release will enjoy the short video biography of Gregor Mendel, the 19th-century father of genetics whose work was largely ignored until well into the 20th century, genetics today is much more complicated

Biologists will of course continue to talk about genes in the future. But genes will no longer be seen as the blueprint for life, even if technological and medical applications of gene technology suggest this. Instead, they are increasingly seen as only one of the many resources that organisms make use of in adapting to challenges in their environments.

Conclusion

The old genetics of the late 20th century was powerful enough evidence of intelligent design, with its systems of highly-accurate transcription and translation of encoded information. Now, we find that the old picture was far too simplistic. And the surprising lack of “genes” found by the Human Genome Project, feeding rumors of useless “junk” pervading our genome, is rapidly being supplanted by evidence of hierarchical codes and functions everywhere. 

If the old genetics was sufficient to allow A.E. Wilder-Smith to help convince Matti Leisola to become a Darwin  Heretic in the 1970s (pp. 40-41), how much more will the flood of new discoveries, illustrated by these few examples, persuade the next generation of geneticists that Darwinism is hopelessly inadequate to account for the complexity of life? It’s like having to account for half a dozen codes instead of one. The future looks bright for ID in next-generation genetics, embedded in epigenetics. The nucleus is a whole new ball game.

And still yet more proto-life v. Darwin.

Molecular Machine Menagerie Brightens
Evolution News & Views 

In 1998, former AAAS president Bruce Alberts contemplated what "the next generation of molecular biologists" needed to study. Evidence had been mounting that proteins don't just undergo chemical reactions, but actually perform physical work with moving parts. "Indeed," he said in the journal Cell, "the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines."

At the time, he acknowledged that "we still have an enormous amount to learn," but also invited young molecular biologists to engage the factory metaphor, saying, "the great future in biology lies in gaining a detailed understanding of the inner workings of the cell's many marvelous protein machines." Now, almost twenty years later, the lights on this factory are much brighter. Let's look at some of the machinery with the unprecedented detail provided by advances in imaging.

Kinesin with gear switch. What's more machine-like than gears? One of the kinesin "walking" motors has a gear switch that lets it change direction. This impressed molecular biologists at Oregon State. We read, "Scientists discover a molecular motor has a 'gear' for directional switching." The particular kinesin, named KlpA, helps pull chromosomes apart during cell division. Most kinesins are like one-way roller-coaster cars on their tracks, but this one "contains a gear-like component that enables it to switch direction of movement."

"KlpA is a fascinating motor protein because it is the first of its kind to demonstrate bidirectional movement," [Weihong] Qiu said. "It provides a golden opportunity for us to learn from Mother Nature the rules that we can use to design motor protein-based transport devices. Hopefully in the near future, we could engineer motor protein-based robotics for drug delivery in a more precise and controllable manner." [Emphasis added.]
For more on this amazing molecular machine, see our video, "The Workhorse of the Cell: Kinesin."

Perfectionist editor. Like a picky newspaper editor, the spliceosome goes to work on "text" transcribed from DNA. This large machine has been hard to study because it is so complicated. Two papers in Nature discuss new findings about it. In "Structure of a spliceosome remodelled for exon ligation," Fica and team use words like "lariat" and "attack" to show how the spliceosome spends ATP currency as it docks the target, slices and rotates messenger-RNA 'paragraphs' for rearrangement. In "Cryo-EM structure of a human spliceosome activated for step 2 of splicing," Bertram and team describe how one portion of the complex grabs an intron and a base and moves them out of the catalytic core, thereby opening up space for the exon to dock in the right position before it is spliced in. How this multi-component machine knows what to grab, where to position it, and what sequence to follow should strike anyone as fascinating. It's a molecule, but it acts like a precision robot with moving parts!

Power walkers. Myosins comprise a family of transport machines that use a hand-over-hand 'walking' motion. Labeled with Roman numerals, such as myosin-VI, they perform numerous important functions in the cell. In recent weeks, four papers about myosins appeared in the Proceedings of the National Academy of Sciences. First, a review of the other papers by Citovsky and Liu compares the activity of myosins in animals vs plants, finding surprises in how unique the myosins in plants are. Should you care? They think so. They say, "we all should care for the workings of the plant cell because plants sustain life on Earth."

Elizabeth Kurth is joined by Eugene Koonin and others in a paper about "Myosin-driven transport network in plants," focusing on myosin-IX involved in the 'cytoplasmic streaming' so characteristic of plant cells. They find hints of "a myosin-dependent nucleocytoplasmic trafficking pathway."

Mukherjee and two others describe the "dynamics of the mechanochemical cycle of myosin-V" with descriptive terms like powerstroke, hand-over-hand motion, and force generation.

French, Sosnick, and Rock investigate "human myosin VI targeting using optogenetically controlled cargo loading." To watch these motors, they tagged their cargoes with glowing molecules and found new clues to how the cargoes cooperate with the motors and signal each other in a site-specific manner. "Myosins play countless critical roles in the cell, each requiring it to be activated at a specific location and time," they say.

Speaking of walking machines, if the smart guys at Purdue University design a molecular walking machine made of DNA that we know is intelligently designed, is it fair to attribute intelligent design to the natural walkers in the cell that perform much better? Yet they say, "The designs are inspired by natural biological motors that have evolved to perform specific tasks critical to the function of cells." Go figure.

Dedicated translator. We know about the ribosome--one of the most intricate machines in the cell -- with its RNA and protein parts that translate messenger RNA into proteins. But did you know that mitochondria (the power plants of the cell) have dedicated ribosomes that are smaller? In Science Magazine, a European team studied the "mitoribosome" in yeast and found that it has a distinct architecture, including a large RNA component and 34 proteins, "including 14 without homologs in the evolutionarily related bacterial ribosome." (How they know it is "evolutionarily related" if it is so different is a conundrum for another time.) Like cytoplasmic ribosomes, the mitoribosome threads messenger RNAs into an entrance channel into the interior, where transfer RNAs line up their corresponding amino acids into proteins. Then the mRNA strand is fed out an exit channel, where folding begins. The team found that the mitoribosome adopts three distinct conformations as it works, but with more subtle motions than the cytoplasmic ribosomes.

Turnstiles. Channels form a large, important class of molecular machines. These are the gates embedded in membranes for purposes of import and export: i.e., "active transport" that goes against the concentration gradient to give a cell control of its interior. Each channel is specific for its own type of molecule: some for ions, some for nutrients, some for expelling toxins, and more. Channels employ several types of "selectivity filters" to ensure only the correct molecules get through.

Researchers at Ludwig Maximilian University in Munich reported on "adaptor proteins" that act like tickets for getting through certain channels that control the flow of sodium and calcium ions. They "uncovered an activation mechanism in which an accessory molecular adaptor acts as a fail-safe mechanism to prevent inappropriate opening of two related ion channels." The details are published in PNAS.

Roderick MacKinnon, who won a Nobel Prize for his work on ion channels, is back with two colleagues describing more details on how a high-throughput calcium-ion channel guarantees passage to only the correct ions. Writing in Nature, they begin, "The precise control of an ion channel gate by environmental stimuli is crucial for the fulfilment of its biological role." That precision is maintained by moving parts in the selectivity filter "through covalent linkers and through protein interfaces formed between the gating ring and the voltage sensors." Consequently, membrane voltage regulates the gating of the pore by influencing calcium-ion sensors. A second paper by the team in Nature describes the structure of the high-conductance potassium channel.

A team of three at University of Texas describes how "two-pore channels" tune their selectivity filters. Writing in PNAS, they first mention that these two-pore channels are ubiquitous throughout the living world. "Interestingly," they remark, "plant and animal TPCs share high sequence similarity in the filter region, yet exhibit drastically different ion selectivity." In one mutation experiment, a change of one amino acid changed the filter's selectivity from potassium to sodium. In another case, "the carboxamide groups of the two symmetrical Asn630 residues are in a defined position with less mobility, allowing them to exert stringent size selection for the crossing ions."

Well, we're out of space for this quick tour of the molecular machine menagerie, but not out of examples. More tomorrow. Some take-home lessons so far:

Each machine is extremely well built for its function.

The machines are very complex, consisting of multiple protein and/or RNA molecules.

They often have moving parts that interact with other machines in precise ways.

They work in specific locations at specific times.

Minor changes can have deleterious effects, or even cause failure.

'Fail-safe' mechanisms ensure proper operation.

They are built from complex specified information in genes.

That list has intelligent design written all over it.

And still yet more proto-life v. Darwin II

More Marvels in the Molecular Machine Menagerie
Evolution News & Views

As a plausible explanation of life's complexity, Darwinian thinking emerged when cellular biology was a great blur. As what we know about cells and their contents has dramatically sharpened in detail and focus, orthodox evolutionary thinking correspondingly fades in its persuasiveness. That's a lesson of what we wrote yesterday on molecular machines ("Molecular Machine Menagerie Brightens"), but the latest news on that theme can't be encompassed by a single article, or two. Therefore we move on to automated security agents, linemen, recyclers, thermostats, assemblers, inspectors, bodyguards, and more.

Addendum on ion channels. Here's another new paper about voltage-gated sodium channels, called Navs. In humans, these are involved in sensory neurons as well as heart and brain cells, but even microbes have them. We'll share one quick quote from the paper in Nature Communications :

The cycling of Navs through open, closed and inactivated states, and their closely choreographed relationships with the activities of other ion channels lead to exquisite control of intracellular ion concentrations in both prokaryotes and eukaryotes. [Emphasis added.]
Skilled linemen. Researchers at the  Technical University of Darmstadt were surprised to learn that the machines that repair double-stranded breaks in DNA are "far more complex than previously assumed." For instance, "The ends of breaks in the double helix are not just joined, they are first changed in a meticulously choreographed process so that the original genetic information can be restored." Interesting that both the above entries refer to choreography -- a great design word suggesting irreducible complexity -- augmenting the impact with the adjectives exquisite and meticulous.

No-nonsense chaperone. You can see another machine's structure in 3-D at Caltech News, where the article states, "Protein chaperone takes its job seriously." What is it? It's a ribosomal protein's secret service bodyguard, essentially:

For proteins, this would be the equivalent of the red-carpet treatment: each protein belonging to the complex machinery of ribosomes -- components of the cell that produce proteins -- has its own chaperone to guide it to the right place at the right time and protect it from harm.
The particular protein they studied, named L4, has a chaperone that fits tightly like a hand and glove. When the protein is produced in the nucleus, the chaperone takes it on a long trip out the nuclear pore and into the cytoplasm, where it has to be fitted into the ribosome at the right place and time. Along the way, the chaperone protects its client from being chopped up by the "protein-shredding machinery." This article is loaded with amazing facts. For example,

Building ribosomes is a formidable undertaking for the cell, involving about 80 proteins that make up the ribosome itself, strings of ribosomal RNA, and more than 200 additional proteins that guide and regulate the process. "Ribosome assembly is a dynamic process, where everything happens in a certain order. We are only now beginning to elucidate the many steps involved," says [André] Hoelz.
That's a picture of choreography again. One more little factoid if you're not impressed yet: "More than a million ribosomes are produced per day in an animal cell." This is one big ballet!

The Shredder. The article above mentioned "protein-shredding machinery," so let's see what's new about that. A European team publishing in the  Proceedings of the National Academy of Sciences  has learned that the 26S Proteosome, "a large multisubunit complex that executes the degradation of intracellular proteins marked for destruction," contains an "engine" with moving parts. This engine "unfolds and translocates substrates into the 20S core particle" where the protein is shredded, allowing its amino acids to be recycled. How does the machine know what to recycle? Mistakes could be disastrous, harming working proteins. For proper identification, other machines "tag" the trash with ubiquitin molecules. The proteasome checks the tags before letting the protein into the recycling bin. We've all seen the trucks that lift trash cans into big bins and shake them. Something like that goes on in the cell:

Here, we report cryo-EM structures of the yeast 26S proteasome in the presence of different nucleotides and nucleotide analogs, revealing the existence of four distinct conformational states. These structures elucidate the conformational changes underlying substrate translocation and their coupling with gate opening.
This is no clunky trash truck. Processing involves multiple steps, gate openings, twists and turns in a specific sequence, all requiring ATP for energy. "We assume that the cycle continues until the substrate translocation process is finished," they say in conclusion. "Our structures favor a model in which the hydrolysis cycle occurs in a sequential order around the ring rather than in a stochastic manner." Interestingly, one of the positions they call the "lockwasher conformation." There could well be additional dance steps of this cellular robot that haven't been discovered yet.

Inspector-Ejectors to the rescue. In the ribosome, messenger RNAs are translated into proteins. What if the mRNA has a typo? What if it lacks a stop codon? The resulting protein could be damaged, or even dangerous. "The ability to dispose of proteins that are either aberrant or (in the worst case) toxic is fundamental to a cell's survival, says news from  Charité University of Medicine in Berlin.. Researchers describe "rescue proteins" that patrol ribosomes, providing the necessary quality control on the assembly line. The next question is: how do they recognize errors?

Using cryo-electron microscopy to study the structure of such ribosome-mRNA complexes, the researchers were able to show the manner in which special rescue proteins (Dom34 and Hbs1) recognize such stalled ribosomes, thereby initiating the splitting of the arrested complex and the degradation of the faulty mRNA. The rescue proteins recognize arrested ribosomes by detecting, and binding to, conserved locations normally occupied by mRNA. This direct competition-based approach ensures that only ribosomes with aberrant mRNAs are targeted.
The Stapler. Briefly, an article from Ludwig Maximilian University  of Munich describes protein machines that attach to mRNAs as they exit the nucleus and stabilizes them for transport. "We were surprised to see that the RNA is not only recognized by these proteins, they also force it to adopt a new form. They staple it together, so to speak." Then the motor proteins "take the mRNA train," carrying the passenger down the cell's "railway lines," the article says picturesquely.

Pressure thermostat. How do epithelial tissues maintain the right number of cells? Researchers at the University of Utah  wanted to know. First, they found that simple mechanical tension affects the balance of birth and death. When cells get too crowded, internal pushing forces lead some cells to pop out of the tissue and die, undergoing apoptosis. When cells get too sparse, they pull on each other, triggering cell division and the creation of new cells to fill in the gaps. But then, they discovered a protein machine responsible for this balance. It's called Piezo1, named undoubtedly for its mechanosensitive nature, like certain crystals that can spark when compressed. Piezo1 acts like a "thermostat" on both sides of the cell, they found.

Just like a thermostat regulates both heat and cold, it makes sense to have one sensor measuring crowding and stretch. If there were two separate regulators, things could get out of hand fairly quickly if one sensor breaks.
Fancy footwork. Did you know some cells have feet? Cells in your immune system, for instance, create about a hundred "podosomes" (foot bodies) to move quickly to their sites of operation. The podosomes secrete proteins that degrade the extracellular matrix, allowing the immune cells to slip through crowded tissues. Researchers at the  National University of Singapore wanted to learn more about how cells form these little feet. What they found was too complex to describe in detail here, but it involves multiple proteins that form rings, switches and controllers, with the aid of those myosin motors we learned about last time.

The propeller. We lack space to describe the helical zipper (Science Daily), the DNA surgeon (Phys.org) and other fascinating machines, but our mini-tour of the molecular machine menagerie wouldn't seem complete without some news on the iconic bacterial flagellum that was so influential in the intelligent design movement. Two recent papers shed more light on the flagellum, both from osaka university, an institution that has taken the lead on elucidating this propeller's physical secrets in great detail. One news item from Osaka University   explores how pH in the system affects energy when the cell extrudes proteins out of the protein to build the machine. Tiny pH microprobes allowed the team to "propose that the export apparatus uses both ATP hydrolysis as well as H+ differentials to achieve protein export."

The other paper, published by Nature Communications , explores the rod and hook regions of the flagellum. Osaka researchers found that "identical folds" in subunit proteins FlgE and FlgG are "used for distinct mechanical functions" of the rod and hook, which are directly connected to each other. Though these two proteins share 39 percent sequence identity, they have distinct properties: the rod is straight, but the hook is flexible, allowing it to bend as a universal joint. "While these two structures have the same helical symmetry and repeat distance and nearly identical folds of corresponding domains, the domain orientations differ by ∼7°, resulting in tight and loose axial subunit packing in the rod and hook, respectively, conferring the rigidity on the rod and flexibility on the hook," they explain. "This provides a good example of versatile use of a protein structure in biological organisms." That sounds like a good design.

As we said in yesterday's post, there's nothing like investigating machines in detail to reinforce the conviction that cells are intelligently designed; they could not have emerged by blind processes of random mutations and natural selection. Some of these machines, when mutated, result in devastating diseases, like ALS and cancer. Little do we know how much our lives depend on precise, reliable action of actual machines with moving parts on the nanoscale that bear uncanny resemblances to machines we know on the human scale: trash compactors, inspectors, propellers, and much more.

In  Unlocking the Mystery of Life, Jed Macosko said there were "a host of machines" in the cell, as many as there are functions in the human body. Here in 2017, 15 years later, we can see that was no exaggeration. The fuzzier glimpses of machines that turned  Michael Behe into an advocate of intelligent design still have the power to inspire a new generation of young scientists -- all the more so with the increasing resolution of advanced imaging techniques.

On the Church fathers and the one true God

Problem solving like a Titan.

Wannabe Titans?

A clash of Titans. LXXI

Scientists routinely employ design filters.

Yes, Intelligent Design Is Detectable by Science

Stephen C. Meyer

Editor’s note: The online journal Sapientia recently posed a good question to several participants in a forum: “Is Intelligent Design Detectable by Science?” This is one key issue on which proponents of ID and of theistic evolution differ. Stephen Meyer, philosopher of science and director of Discovery Institute’s Center for Science & Culture, gave the following reply.

Biologists have long recognized that many organized structures in living organisms — the elegant form and protective covering of the coiled nautilus; the interdependent parts of the vertebrate eye; the interlocking bones, muscles, and feathers of a bird wing — “give the appearance of having been designed for a purpose.”1

Before Darwin, biologists attributed the beauty, integrated complexity, and adaptation of organisms to their environments to a powerful designing intelligence. Consequently, they also thought the study of life rendered the activity of a designing intelligence detectable in the natural world.

Yet Darwin argued that this appearance of design could be more simply explained as the product of a purely undirected mechanism, namely, natural selection and random variation. Modern neo-Darwinists have similarly asserted that the undirected process of natural selection and random mutation produced the intricate designed-like structures in living systems. They affirm that natural selection can mimic the powers of a designing intelligence without itself being guided by an intelligent agent. Thus, living organisms may look designed, but on this view, that appearance is illusory and, consequently, the study of life does not render the activity of a designing intelligence detectable in the natural world. As Darwin himself insisted, “There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course in which the wind blows.”2 Or as the eminent evolutionary biologist Francisco Ayala has argued, Darwin accounted for “design without a designer” and showed “that the directive organization of living beings can be explained as the result of a natural process, natural selection, without any need to resort to a Creator or other external agent.”3

But did Darwin explain away all evidence of apparent design in biology? Darwin attempted to explain the origin of new living forms starting from simpler pre-existing forms of life, but his theory of evolution by natural selection did not even attempt to explain the origin of life — the simplest living cell — in the first place. Yet there is now compelling evidence of intelligent design in the inner recesses of even the simplest living one-celled organisms. Moreover, there is a key feature of living cells — one that makes the intelligent design of life detectable — that Darwin didn’t know about and that contemporary evolutionary theorists have not explained away.

The Information Enigma

In 1953 when Watson and Crick elucidated the structure of the DNA molecule, they made a startling discovery. The structure of DNA allows it to store information in the form of a four-character digital code. Strings of precisely sequenced chemicals called nucleotide bases store and transmit the assembly instructions — the information — for building the crucial protein molecules and machines the cell needs to survive.

Francis Crick later developed this idea with his famous “sequence hypothesis” according to which the chemical constituents in DNA function like letters in a written language or symbols in a computer code. Just as English letters may convey a particular message depending on their arrangement, so too do certain sequences of chemical bases along the spine of a DNA molecule convey precise instructions for building proteins. The arrangement of the chemical characters determines the function of the sequence as a whole. Thus, the DNA molecule has the same property of “sequence specificity” that characterizes codes and language.

Moreover, DNA sequences do not just possess “information” in the strictly mathematical sense described by pioneering information theorist Claude Shannon. Shannon related the amount of information in a sequence of symbols to the improbability of the sequence (and the reduction of uncertainty associated with it). But DNA base sequences do not just exhibit a mathematically measurable degree of improbability. Instead, DNA contains information in the richer and more ordinary dictionary sense of “alternative sequences or arrangements of characters that produce a specific effect.” DNA base sequences convey instructions. They perform functions and produce specific effects. Thus, they not only possess “Shannon information,” but also what has been called “specified” or “functional information.”

Like the precisely arranged zeros and ones in a computer program, the chemical bases in DNA convey instructions by virtue of their specific arrangement — and in accord with an independent symbol convention known as the “genetic code.” Thus, biologist Richard Dawkins notes that “the machine code of the genes is uncannily computer-like.”4 Similarly, Bill Gates observes that “DNA is like a computer program, but far, far more advanced than any software we’ve ever created.”5 Similarly, biotechnologist Leroy Hood describes the information in DNA as “digital code.”6

After the early 1960s, further discoveries revealed that the digital information in DNA and RNA is only part of a complex information processing system — an advanced form of nanotechnology that both mirrors and exceeds our own in its complexity, design logic, and information storage density.

Where did the information in the cell come from? And how did the cell’s complex information processing system arise? These questions lie at the heart of contemporary origin-of-life research. Clearly, the informational features of the cell at least appear designed. And, as I show in extensive detail in my book Signature in the Cell, no theory of undirected chemical evolution explains the origin of the information needed to build the first living cell.7

Why? There is simply too much information in the cell to be explained by chance alone. And attempts to explain the origin of information as the consequence of pre-biotic natural selection acting on random changes inevitably presuppose precisely what needs explaining, namely, reams of pre-existing genetic information. The information in DNA also defies explanation by reference to the laws of chemistry. Saying otherwise is like saying a newspaper headline might arise from the chemical attraction between ink and paper. Clearly something more is at work.

Yet, the scientists who infer intelligent design do not do so merely because natural processes — chance, laws, or their combination — have failed to explain the origin of the information and information processing systems in cells. Instead, we think intelligent design is detectable in living systems because we know from experience that systems possessing large amounts of such information invariably arise from intelligent causes. The information on a computer screen can be traced back to a user or programmer. The information in a newspaper ultimately came from a writer — from a mind. As the pioneering information theorist Henry Quastler observed, “Information habitually arises from conscious activity.”8

This connection between information and prior intelligence enables us to detect or infer intelligent activity even from unobservable sources in the distant past. Archeologists infer ancient scribes from hieroglyphic inscriptions. SETI’s search for extraterrestrial intelligence presupposes that information imbedded in electromagnetic signals from space would indicate an intelligent source. Radio astronomers have not found any such signal from distant star systems; but closer to home, molecular biologists have discovered information in the cell, suggesting — by the same logic that underwrites the SETI program and ordinary scientific reasoning about other informational artifacts — an intelligent source.

DNA functions like a software program and contains specified information just as software does. We know from experience that software comes from programmers. We know generally that specified information — whether inscribed in hieroglyphics, written in a book, or encoded in a radio signal — always arises from an intelligent source. So the discovery of such information in the DNA molecule provides strong grounds for inferring (or detecting) that intelligence played a role in the origin of DNA, even if we weren’t there to observe the system coming into existence.

The Logic of Design Detection

In The Design Inference, mathematician William Dembski explicates the logic of design detection. His work reinforces the conclusion that the specified information present in DNA points to a designing mind.

Dembski shows that rational agents often detect the prior activity of other designing minds by the character of the effects they leave behind. Archaeologists assume that rational agents produced the inscriptions on the Rosetta Stone. Insurance fraud investigators detect certain “cheating patterns” that suggest intentional manipulation of circumstances rather than a natural disaster. Cryptographers distinguish between random signals and those carrying encoded messages, the latter indicating an intelligent source. Recognizing the activity of intelligent agents constitutes a common and fully rational mode of inference.

More importantly, Dembski explicates criteria by which rational agents recognize or detect the effects of other rational agents, and distinguish them from the effects of natural causes. He demonstrates that systems or sequences with the joint properties of “high complexity” (or small probability) and “specification” invariably result from intelligent causes, not chance or physical-chemical laws.9 Dembski noted that complex sequences exhibit an irregular and improbable arrangement that defies expression by a simple rule or algorithm, whereas specification involves a match or correspondence between a physical system or sequence and an independently recognizable pattern or set of functional requirements.

By way of illustration, consider the following three sets of symbols:

nehya53nslbyw1`jejns7eopslanm46/J

TIME AND TIDE WAIT FOR NO MAN

ABABABABABABABABABABAB

The first two sequences are complex because both defy reduction to a simple rule. Each represents a highly irregular, aperiodic, improbable sequence. The third sequence is not complex, but is instead highly ordered and repetitive. Of the two complex sequences, only the second, however, exemplifies a set of independent functional requirements — i.e., is specified.

English has many such functional requirements. For example, to convey meaning in English one must employ existing conventions of vocabulary (associations of symbol sequences with particular objects, concepts, or ideas) and existing conventions of syntax and grammar. When symbol arrangements “match” existing vocabulary and grammatical conventions (i.e., functional requirements), communication can occur. Such arrangements exhibit “specification.” The sequence “Time and tide waits for no man” clearly exhibits such a match, and thus performs a communication function.

Thus, of the three sequences only the second manifests both necessary indicators of a designed system. The third sequence lacks complexity, though it does exhibit a simple periodic pattern, a specification of sorts. The first sequence is complex, but not specified. Only the second sequence exhibits both complexity and specification. Thus, according to Dembski’s theory of design detection, only the second sequence implicates an intelligent cause — as our uniform experience affirms.

In my book Signature in the Cell, I show that Dembski’s joint criteria of complexity and specification are equivalent to “functional” or “specified information.” I also show that the coding regions of DNA exemplify both high complexity and specification and, thus not surprisingly, also contain “specified information.” Consequently, Dembski’s scientific method of design detection reinforces the conclusion that the digital information in DNA indicates prior intelligent activity.

So, contrary to media reports, the theory of intelligent design is not based upon ignorance or “gaps” in our knowledge, but on scientific discoveries about DNA and on established scientific methods of reasoning in which our uniform experience of cause and effect guides our inferences about the kinds of causes that produce (or best explain) different types of events or sequences.

Anthropic Fine Tuning

The evidence of design in living cells is not the only such evidence in nature. Modern physics now reveals evidence of intelligent design in the very fabric of the universe. Since the 1960s physicists have recognized that the initial conditions and the laws and constants of physics are finely tuned, against all odds, to make life possible. Even extremely slight alterations in the values of many independent factors — such as the expansion rate of the universe, the speed of light, and the precise strength of gravitational or electromagnetic attraction — would render life impossible. Physicists refer to these factors as “anthropic coincidences” and to the fortunate convergence of all these coincidences as the “fine-tuning of the universe.”

Many have noted that this fine-tuning strongly suggests design by a pre-existent intelligence. Physicist Paul Davies has said that “the impression of design is overwhelming.”10 Fred Hoyle argued that, “A common sense interpretation of the facts suggests that a superintellect has monkeyed with physics, as well as chemistry and biology.”11 Many physicists now concur. They would argue that — in effect — the dials in the cosmic control room appear finely-tuned because someone carefully fine-tuned them.

To explain the vast improbabilities associated with these fine-tuning parameters, some physicists have postulated not a “fine-tuner” or intelligent designer, but the existence of a vast number of other parallel universes. This “multiverse” concept also necessarily posits various mechanisms for producing these universes. On this view, having some mechanism for generating new universes would increase the number of opportunities for a life-friendly universe such as our own to arise — making ours something like a lucky winner of a cosmic lottery.

But advocates of these multiverse proposals have overlooked an obvious problem. The speculative cosmologies (such as inflationary cosmology and string theory) they propose for generating alternative universes invariably invoke mechanisms that themselves require fine-tuning, thus begging the question as to the origin of that prior fine-tuning. Indeed, all the various materialistic explanations for the origin of the fine-tuning — i.e., the explanations that attempt to explain the fine-tuning without invoking intelligent design — invariably invoke prior unexplained fine-tuning.

Moreover, as Jay Richards has shown,12 the fine-tuning of the universe exhibits precisely those features — extreme improbability and functional specification — that invariably trigger an awareness of, and justify an inference to, intelligent design. Since the multiverse theory cannot explain fine-tuning without invoking prior fine-tuning, and since the fine-tuning of a physical system to accomplish a propitious end is exactly the kind of thing we know intelligent agents do, it follows that intelligent design stands as the best explanation for the fine-tuning of the universe.

And that makes intelligent design detectable in both the physical parameters of the universe and the information-bearing properties of life.

Notes:

Richard Dawkins, The Blind Watchmaker (New York, NY: Norton, 1986), 1.

Charles Darwin, The Life and Letters of Charles Darwin, ed. Francis Darwin, vol. 1 (New York: Appleton, 1887), 278–279.

Francisco J. Ayala, “Darwin’s Greatest Discovery: Design without Designer,” Proceedings of the National Academy of Sciences USA 104 (May 15, 2007): 8567–8573.

Richard Dawkins, River out of Eden: A Darwinian View of Life (New York: Basic, 1995), 17.

Bill Gates, The Road Ahead (New York: Viking, 1995), 188.

Leroy Hood and David Galas, “The Digital Code of DNA.” Nature 421 (2003), 444-448.

Stephen Meyer, Signature in the Cell: DNA and the Evidence for Intelligent Design (San Francisco: HarperOne, 2009), 173-323.

Henry Quastler, The Emergence of Biological Organization (New Haven: Yale UP, 1964), 16.

William Dembski, The Design Inference: Eliminating Chance Through Small Probabilities (Cambridge: Cambridge University Press, 1998), 36-66.

Paul Davies, The Cosmic Blueprint (New York: Simon & Schuster, 1988), 203.

Fred Hoyle, “The Universe: Past and Present Reflections.” Annual Review of Astronomy and Astrophysics 20 (1982): 16.

Guillermo Gonzalez and Jay Richards, The Privileged Planet: How Our Place in the Cosmos is Designed for Discovery (Washington, DC: Regnery Publishing, 2004), 293-311.

Photosynthesis v. Darwin.

New Ideas on the Evolution of Photosynthesis Reaction Centers
Cornelius Hunter

Evolutionists do not have a clear understanding of how photosynthesis arose, as evidenced by a new paper  from Kevin Redding’s laboratory at Arizona State University which states:

After the Type I/II split, an ancestor to photosystem I fixed its quinone sites and then heterodimerized to bind PsaC as a new subunit, as responses to rising O2 after the appearance of the oxygen-evolving complex in an ancestor of photosystem II. These pivotal events thus gave rise to the diversity that we observe today.

That may sound like hard science to the uninitiated, but it isn’t.

The Type I/II split is a hypothetical event for which the main evidence is the belief that evolution is true. In fact, according to the science, it is astronomically unlikely that photosynthesis evolved, period.

And so, in typical fashion, the paper presents a teleological (“and then structure X evolved to achieve Y”) narrative to cover over the absurdity:

and then heterodimerized to bind PsaC as a new subunit, as responses to rising O2 …

First, let’s reword that so it is a little clearer: The atmospheric oxygen levels rose and so therefore the reaction center of an early photosynthesis system heterodimerized in order to bind a new protein (which helps with electron transfer).

This is a good example of the Aristotelianism that pervades evolutionary thought. This is not science, at least in the modern sense. And as usual, the infinitive form (“to bind”) provides the telltale sign. In other words, a new structure evolved as a response to X (i.e., as a response to the rising oxygen levels) in order to achieve Y (i.e., to achieve the binding of a new protein, PsaC).

But it gets worse. Note the term: “heterodimerized.” A protein machine that consists of two identical proteins mated together is referred to as a “homodimer.” If two different proteins are mated together it is a “heterodimer.” In some photosynthesis systems, at the core of the reaction center is a homodimer. More typically, it is a heterodimer.

The Redding paper states that the ancient photosynthesis system “heterodimerized.” In other words, it switched, or converted, the protein machine from a homodimer to a heterodimer (in order to bind PsaC). The suffix “ize,” in this case, means to cause to be or to become. The ancient photosynthesis system caused the protein machine to become a heterodimer.

Such teleology reflects evolutionary thought and let’s be clear — this is junk science. From a scientific perspective there is nothing redeeming here. It is pure junk.

But it gets even worse.

These pivotal events thus gave rise to the diversity that we observe today.

Or as the press release described it:

Their [reaction centers’] first appearance and subsequent diversification has allowed photosynthesis to power the biosphere for over 3 billion years, in the process supporting the evolution of more complex life forms.

So evolution created photosynthesis which then, “gave rise to” the evolution of incredibly more advanced life forms. In other words, evolution climbed an astronomical entropic barrier and created incredibly unlikely structures which were crucial for the amazing evolutionary history to follow.

The serendipity is deafening.