Ann Gauger

[anngauger]

The Nylonase Story: When Imagination and Facts Collide

Editor’s note: Nylon is a modern synthetic product used in the manufacturing, most familiarly, of ladies’ stockings but also a range of other goods, from rope to parachutes to auto tires. Nylonase is a popular evolutionary icon, brandished by theistic evolutionist Dennis Venema among others. In a series of three posts, Discovery Institute biologist Ann Gauger takes a closer look.

A significant problem for the neo-Darwinian story is the origin of new biological information. Clearly, information has increased over the course of life’s history — new life forms appeared, requiring new genes, proteins, and other functional information. The question is — how did it happen? This is the central question concerning the origin of living things.

Stephen Meyer and Douglas Axe have made this strong claim:

[T]he neo-Darwinian mechanism — with its reliance on a random mutational search to generate novel gene sequences — is not an adequate mechanism to produce the information necessary for even a single new protein fold, let alone a novel animal form, in available evolutionary deep time.

Their claim is based on the experimental finding by Doug Axe that functional protein folds are exceedingly rare, on the order on 1 in 10 to the 77th power, meaning that all the creatures of the Earth searching for the age of the Earth by random mutation could not find even one medium-size protein fold.

In contrast, Dennis Venema, professor of biology at Trinity Western University, claims in his book Adam and the Genome and in posts at the BioLogos website that getting new information is not hard. In his book, he presents several examples he thinks demonstrate the appearance of new information — the apparent evolution of new protein binding sites, for example. But the best way to reveal Axe and Meyer’s folly, he thinks, (and says so in his book and a post at BioLogos) would be to show that a genuinely “new” protein can evolve.

…[E]ven more convincing… would be an actual example of a functional protein coming into existence from scratch — catching a novel protein forming “in the act” as it were. We know of such an example — the formation of an enzyme that breaks down a man-made chemical.

In the 1970s, scientists made a surprising discovery: a bacterium that can digest nylon, a synthetic chemical not found in nature. These bacteria were living in the wastewater ponds of chemical factories, and they were able to use nylon as their only source of food. Nylon, however, was only about 40 years old at the time — how had these bacteria adapted to this novel chemical in their environment so quickly? Intrigued, the scientists investigated. What they discovered was that the bacteria had an enzyme (which they called “nylonase”) that effectively digested the chemical. This enzyme, interestingly, arose from scratch as an insertion mutation into the coding sequence of another gene. This insertion simultaneously formed a “stop” codon early in the original gene (a codon that tells the ribosome to stop adding amino acids to a protein) and formed a brand new “start” codon in a different reading frame. The new reading frame ran for 392 amino acids before the first “stop” codon, producing a large, novel protein. As in our example above, this new protein was based on different codons due to the frameshift. It was truly “de novo” — a new sequence.

Venema is right. If the nylonase enzyme did evolve from a frameshifted protein, it would genuinely be a demonstration that new proteins are easy to evolve. It would be proof positive that intelligent design advocates are wrong, that it’s not hard to get a new protein from random sequence. But the story bears reexamining. Is the new protein really the product of a frameshift, or did it pre-exist the introduction of nylon into the environment? What exactly do we know about this enzyme? Does the evidence substantiate the claims of Venema and others, or does it lead to other conclusions?

First, some history. In the 1970s Japanese scientists discovered that certain bacteria had developed the ability to degrade the synthetic polymer nylon. Okada et al. identified three enzymes responsible for nylon degradation, and named them EI, EII, and EIII. The genes that encoded them were named nylA,nylB, and nylC. They sequenced the plasmid on which the genes were found, and discovered that there was another gene on the same plasmid that was very similar to nylB; they named it nylB′. (We will focus on the story of nylB and nylB′ because they are the ones relevant to Venema’s story.)

So far all I have given you are the facts. Now here’s the interpretation of these facts. Some claimed that the nylonase enzyme, as it was called, had originated some time after people began making nylon (in the 1930s). That seemed plausible because nylonase was unable to degrade naturally occurring amide bonds — it could degrade only the amide bonds in nylon — and so had not existed previously, it was thought. The popular conclusion was that the nylonase activity evolved in response to the presence of nylon in the environment, and thus was only forty years old. And here’s the big interpretive leap: it must not be hard to get new enzymes if a new one can evolve within a period of forty years.

Okada et al. had sequenced the genes encoding nylB and nylB′. They concluded that the nylonase activity was the result of a gene duplication followed by several mutations to the nylB gene. But at this point Susumu Ohno, an eminent molecular geneticist and evolutionary biologist, noticed something unusual about the nylB gene sequence (Ohno, 1984). Ohno had a theory that DNA with repeats of the right kind had the potential to code for protein in multiple frames, with no interrupting stop codons, and might thus be a source for “new” proteins. (If you are unfamiliar with the terms I just used, I invite you to take a look at my post tomorrow, where I will explain the necessary concepts. For those already familiar, I present some relevant data concerning the rarity of sequences that can be frameshifted.)

Ohno noticed that nylB, the gene for nylonase, might originally have encoded something else if a certain T was removed. The nylonase gene as it exists now has 1179 bases, which encode a 392 amino acid protein. Without a particular T embedded in the ATG start codon, though, the sequence would have specified a hypothetical original gene with a longer open reading frame (ORF) of 427 amino acids, in a different frame. Thus, Ohno proposed a “new” protein with a new function acting on a new substrate was born when a T inserted in between a particular A and G in the DNA, making a new ATG start codon and shifting the frame to code for a new protein, the protein we now call nylonase.

Ingenious. According to Ohno, nylonase could be a new enzyme, appearing suddenly with no known precursors via a sudden frameshift. (Note that all of this assumes that new protein folds are easy to get.) Ohno published this hypothesis in the Proceedings of the National Academy of Sciences. It was a hypothesis only, however, as a careful reading of his paper shows. One heading, for example:

R-IIA Coding Sequence [nylB] for 6-AHA LOH [nylonase] Embodies an Alternative, Longer Open Reading Frame That Might Have Been the Original Coding Sequence [Emphasis added.]

and the text says:

I suggest that the RS-IIA base sequence [nylB] was originally a coding sequence for an arginine-rich polypeptide chain 427 or so residues long in its length and that the coding sequence for one of the two isozymic forms of 6-ALA LOH [nylonase] arose from its alternative open reading frame. [Emphasis added.]

Ohno presented arguments for why his suggestion was plausible, but did not provide evidence that the “original” gene ever existed or was used (in fact he says it was unlikely to be useful based on its amino acid composition), or that the insertion ever happened. Nonetheless, the frame-shift hypothesis for the origin of nylonase has been widely proclaimed as fact (though, notably, not by Okada et al. who have done most of the work).

If the nylonase story as told above were true, namely that a frameshift mutation resulted in the de novo generation of a new protein fold with a new function, it would indeed constitute a substantial refutation to Meyer and Axe’s claim. If a frame-shift mutation can produce a random new open reading frame in real, observable time, and give rise to a new functional enzyme, then it must not be that hard to make new functional protein folds. In other words, functional protein folds must not be rare in sequence space. And therefore Stephen Meyer’s arguments about the difficulty of getting enough new biological information to generate a new fold must be wrong as well. Venema flatly asserts:

If de novo protein-coding genes such as nylonase can come into being from scratch, as it were, then it is demonstrably the case that new protein folds can be formed by evolutionary mechanisms without difficulty….[I]f Meyer had understood de novo gene formation — as we have seen, he mistakenly thought it was an unexplained process — he would have known that new protein folds could indeed be easily developed by evolutionary processes.

Slam dunk, right?

A little caution in accepting this story without hard evidence would be wise. In genetics we are taught that frame-shift mutations are extremely disruptive, completely changing the coding sequence and resulting in truncated nonsense. In fact, one term for a frameshift mutation is “nonsense mutation.” A biologist’s basic intuition should be that frameshifts are highly unlikely to produce something useful. The only reasons for the widespread acceptance of Ohno’s hypothesis that I can come up with are the unusual character of the sequence itself, Ohno reputation as a brilliant scientist (which he was), and wish-fulfillment on the part of some evolutionary biologists.

Fortunately, science marches on, and evidence continues to accumulate. The same group of Japanese scientists continued their study of the nylonase genes. nylB appeared to be the result of a gene duplication of nylB′ that occurred some time ago. EII′ (the enzyme encoded by nylB′) had very little nylonase activity, while EII (the enzyme encoded by nylB) was about 1000 fold higher in activity. The two enzymes differed in amino acid sequence at 47 positions out of 392. With some painstaking work, the Japanese determined that just two mutations were sufficient to convert EII′ to the EII level of activity.

They then obtained the three-dimensional structure of an EII-EII′ hybrid protein. And with those results everything changed — or should have.

Here’s what Venema takes from the paper and interprets the evidence:

…the three-dimensional structure of the protein has been solved using X-ray crystallography, a method that gives us the precise shape of the protein at high resolution. Nylonase is chock full of protein folds— exactly the sort of folds Meyer claims must be the result of design because evolution could not have produced them even with all the time since the origin of life. [Emphasis added.]

Unfortunately, Venema doesn’t have the story straight. Nylonase has a particular fold, a particular three-dimensional, stable shape. Most proteins have a distinct fold — there are several thousand kinds of folds known so far, each with a distinct topology and structure. Folds are typically made up of small secondary structures called alpha helices and beta strands, which help to assemble the tertiary structure — the fold as a whole. Venema seems unclear about what a protein fold is, and the distinction between secondary and tertiary structures. Nylonase is not “chock full of folds.” No structural biologist would describe nylonase as “chock full of protein folds.” Indeed, no protein is “chock full of folds.” Perhaps Venema was referring to the smaller units of secondary structure I mentioned above, the alpha helices or beta strands. But it would appear he doesn’t know what a protein fold is.

Maybe that explains why Venema missed the essential point of the paper describing nylonase’s structure. The crystal structure of EII-EII’ (a nylonase hybrid necessary to be able to crystalize the protein) revealed that it is not a new kind of fold, but a member of the beta-lactamase fold family. More specifically, it resembles carboxylesterases, a subgrouping of that family. In addition, when the scientists checked EII′ and EII, they found that both enzymes had previously undetected carboxylesterase activity. In other words, the EII’ and EII enzymes were carboxylesterases. If it looks like a duck and quacks like a duck, it is a duck.

Thus, EII′ and EII did not have frameshifted new folds. They had pre-existing folds with activity characteristic of their fold type. There was no brand-new protein. No novel protein fold had emerged. And no frameshift mutation was required to produce nylonase.

Where did the nylon-eating ability come from? Carboxylesterases are enzymes with broad substrate specificities; they can carry out a variety of reactions. Their binding pocket is large and can accommodate a lot of different substrates. They are “promiscuous” enzymes, in other words. Furthermore, the carboxylesterase reaction hydrolyzes a chemical bond similar to the one hydrolyzed by nylonase. Tests revealed that both the EII and EII′ enzymes have carboxylesterase and nylonase activity. They can hydrolyze both substrates. In fact it is possible both had carboxylesterase activity anda low level of nylonase activity from the beginning, even before the appearance of nylon.

nylB′ may be the original gene from which nylB came. Apparently there was a gene duplication at some point in the past. The two genes appear to have acquired mutations since then — they differ by 47 amino acids out of 392. The time of that duplication is unknown, but not recent, because it takes time to accumulate that many mutations. However, at least some of those mutations must confer a high level of nylonase activity on EII, the enzyme made by nylB. The enzyme EII’ made by nylB’ has only a low ability to degrade nylon, while EII degrades nylon 1000 fold better. So one or more of those 47 amino acid differences must be the cause of the high level of nylonase activity in EII. Through careful work, the Japanese workers Kato et al. identified which amino acid changes were responsible for the increased nylonase activity. Just two step-wise mutations present in EII, when introduced into EII’, could convert the weak enzyme EII’ to full nylonase activity.

From Kato et al. (1991):

Our studies demonstrated that among the 47 amino acids altered between the EII and EII’ proteins, a single amino acid substitution at position 181 was essential for the activity of 6-aminohexanoate-dimer hydrolase [nylonase] and substitution at position 266 enhanced the effect.

So. This is not the story of a highly improbable frame-shift producing a new functional enzyme. This is the story of a pre-existing enzyme with a low level of promiscuous nylonase activity, which improved its activity toward nylon by first one, then another selectable mutation. In other words this is a completely plausible case of gene duplication, mutation, and selection operating on a pre-existing enzyme to improve a pre-existing low-level activity, exactly the kind of event that Meyer and Axe specifically acknowledge as a possibility, given the time and probabilistic resources available. Indeed, the origin of nylonase actually provides a nice example of the optimization of a pre-existing fold’s function, not the innovation or creation of a novel fold.

As the scientists who carried out the structural determination for nylonase themselves note:

Here, we propose that amino acid replacements in the catalytic cleft of a preexisting esterase with the beta-lactamase fold resulted in the evolution of the nylon oligomer hydrolase. [Emphasis added.]

Let’s put to bed the fable that the nylon oligomer hydrolase EII, colloquially known as nylonase, arose by a frame-shift mutation, leading to the creation of a new functional protein fold. There is absolutely no need to postulate such a highly improbable event, and no justification for making this extravagant claim. Instead, there is a much more parsimonious explanation — that nylonase arose by a gene duplication event some time in the past, followed by a series of two mutations occurring after the introduction of nylon into the environment, which increased the nylon oligomer hydrolase activity of the nylB gene product to current levels. Could this series of events happen in forty years? Most certainly. Probably in much less time. In fact, it has been reported to happen in the lab under the right selective conditions. And most definitely, the evolution of nylonase does not call for the creation of a novel protein fold, nor did one arise. EII’s fold is part of the carboxylesterase fold family. Carboxylesterases serve many functions and have been around much longer than forty years.

Douglas Axe and Stephen Meyer readily admit that this kind of evolutionary adaptation happens easily. A protein that already has a low level of activity for a particular substrate can be mutated to favor that side reaction over its original one, often in just a few steps. There are many cases of this in the literature. What Axe and Meyer do claim is that generating an entirely new protein fold via mutation and selection is implausible in the extreme. Nothing in the nylonase story that Dennis Venema tells shows otherwise.

Tomorrow: “The Nylonase Story: How Unusual Is That?”

Photo: Nylon parachute, by Lance Corporal Brian D. Jones, U.S. Marine Corps [Public domain], via Wikimedia Commons.

Originally posted at https://evolutionnews.org/2017/05/the-nylonase-story-when-imagination-and-facts-collide/

[bi010gic]

There is a whole school of research aimed at showing we are not so separate from chimps, and even that they are already on the way up. In a recent BBC article by Colin Barras the focus was on the use of stone tools, and the bold claim that chimps and some monkeys are already in the Stone Age because of their use of rocks as tools.

Some of the reports of stone use appear valid. Capuchins and chimpanzees are all known to use stones to crack open food, and the technique appears to go back thousands of years. But then, no one is disputing that some animals use simple tools. Even otters use stones to break open clam shells.

Then there is the social side. Another BBC article, this one by Melissa Hogenboom, describes ways that chimps show empathy and social awareness, the ability to read facial expressions, to hide things from others, and to share. But then those things are not so unique–anyone who has lived with dogs knows how acutely sensitive to social cues and facial expressions they are, and how they seem to show guilt over bad behavior. They can even share–or be greedy, depending on the dog’s temperament.

And of course, she describes how chimps have the capacity for language. Translation: chimps that have lived and trained with humans can have a vocabulary of 500 words, and can understand thousands more.

But is this a sign they are on the road to becoming like us?

In a further BBC article, Hogenboom lays out the argument against the idea that there is little difference between us and chimps. She quotes Ian Tatersall, a paleoanthropologist at the American Museum of Natural History in New York: “Obviously we have similarities. We have similarities with everything else in nature; it would be astonishing if we didn’t. But we’ve got to look at the differences,”

Hogenboom writes:

When you pull together our unparalleled language skills, our ability to infer others’ mental states and our instinct for cooperation, you have something unprecedented. Us.

‘Just look around you,’ Tomasello [of the Max Planck institute for Evolutionary Anthropology in Leipzig, Germany,] says, 'we’re chatting and doing an interview, they (chimps) are not.’

We have our advanced language skills to thank for that. We may see evidence of basic linguistic abilities in chimpanzees, but we are the only ones writing things down.

We tell stories, we dream, we imagine things about ourselves and others and we spend a great deal of time thinking about the future and analyzing the past.

Not to mention the Brandenburg Concertos. Calculus. Hamlet. The Pythagorean theorem. The discovery of the periodic table. Einstein’s theory of relativity. All works of genius.

In her first article I think Hogenboom overplays the similarities between chimps and humans, just as Barras exaggerates their tool-making ability. Both authors accept the standard Darwinian view, however. Perhaps that accounts for their need to have a story of underlying similarity.

Ms. Hogenboom attributes all this to our big brains in her second article. She does admit that nobody knows how our brains came to be big. Neither does anyone have any solid explanation for how the anatomical, developmental, and physiological differences between us and chimps came to be.

At least Ms. Hogenboom acknowledges there might be a difficulty in explaining things.

Image by Thomas Lersch (Own work) [GFDL , CC-BY-SA-3.0 or CC BY 2.5, via Wikimedia Commons.

[bi010gic]

In 2010 Mike Behe published a paper in the Quarterly Review of Biology in which he concisely stated the first rule of adaptive evolution : “Break or blunt any functional coded element whose loss would yield a net fitness gain.” By this he meant several things. First, there are indeed adaptive mutations, mutations that yield a benefit to the cell under a particular set of circumstances. Second, the primary way such adaptation occurs is by breaking or inactivating some non-essential pre-existing function, in order to make the cell more fit, more competitive than its neighbors.

Behe was talking about microbes –viruses and bacteria–but it also happens at the cellular level in higher organisms. The best example where this rule is played out is in cancer. Cancers develop when one or more normal functions in a cell are disrupted, broken. The ironic thing is that for the cancer cells, this breaking increases their fitness, their rate of growth and cell division, and thus is beneficial—for them. Normal constraints have been removed, allowing uncontrolled growth. For the cancer cell that’s good, but bad for us, of course. So one can say that cancer is a prime example of what adaptive evolution can accomplish on the multicellular level, by breaking or disrupting some normal function.

What does Behe’s first rule of adaptive evolution say about evolution in general? If most “beneficial” mutations are due to the loss of something rather than a gain of something, we are losing information when most adaptations occur, sometimes irreversibly. Let me give an example.

Ralph Seelke and I published a paper in 2010 where we demonstrated that cells always, or nearly always take the easiest road to success. When given a choice between a simple two-step path leading to repair of two genes needed to make tryptophan, versus a one-step path that eliminated expression of the those genes, only one out of a trillion cells went down the path toward making tryptophan, even though that path would ultimately be much more beneficial. Why did this happen? The genes to be repaired were overexpressed—too much of their products were made. Because one of the genes was broken in two places, no tryptophan could be made. Thus both genes were expensive to keep around. It was easier for the cell to break the useless genes than to repair them—one step instead of two—and the cells, having no foresight, took that path. Some of those cells deleted the genes, thus losing the information needed to make tryptophan for good.

Let me explain in every-day terms. A faucet leaking badly but with no way to hook it up to a hose is entirely useless. While it is relatively easy to repair the faucet, requiring only two parts, the owner of the faucet doesn’t know that. Since he can do without the faucet, he is likely to cap the faucet to stop the expense of the wasted water. But he has lost the ability to water his back yard using that faucet.

Like the clueless owner, evolution has no foresight and does not know there is a big pay-off just two mutations away. If the cells can prevent the overexpression of the tryptophan genes or remove them in a single step, that’s what they will do, especially since there are many more ways to inactivate a gene than repair it. Any cell that does this instantly becomes more fit than its neighbors, because it is spending less energy making useless stuff.

In fact, that is what we observed. Nearly all the cells inactivated the genes (only one out of a trillion didn’t). Some of the cells even deleted the genes, thus losing the capacity to make tryptophan for good. Darwinian evolution travels by the shortest road, without regard for where it’s headed. And if the shortest road is to break an existing function–to lose information–that’s the path it chooses.

I’m sure you can think of parallels in the business world, when only the bottom line, corporate fitness, is what matters, and executives have no long-term vision. They don’t see how some things, if adjusted, may yield big pay-offs. As a result, whole technologies can be decimated or lost in a push for efficiency, technologies that if maintained could prove vital in the future. But fortunately, unlike Darwinian evolution, we do have foresight and can plan ahead. We do have the capacity for innovation, and can make wise choices or correct our mistakes.

The process of innovation is the opposite of the first rule of adaptive evolution. In the biological world, the quickest road to adaptation may be to delete or inactivate genes that are not necessary. But you don’t get new features by deleting information. Building something new, which is what is required to explain the diversity around us, requires more than the happenstance and selection of Darwinian evolution. It requires foresight, planning, and a clear picture of the goal. It requires intelligent design.

Image credit: Forest & Kim Starr [CC BY 3.0], via Wikimedia Commons

[bi010gic]

Studying the design of life

By Ann Gauger

What makes us human? Some would say it’s our genes. I don’t want to argue the case that we are more than our genes, which we are. I simply want to point out that interesting new research indicates we have a number of new genes–genes that are specifically human–in our genome.

These new genes are few in number, some would say, but there is a current bias in genome annotation against classifying sequences as novel genes. Estimates range from 3 to 60 to 300 human-specific protein-coding genes. In fact, one genetic analysis came up with 1177 human-specific genes, and then proceded to systematically eliminate them all as non-coding for a variety of reasons, reasons that may or may not be valid. Why does this matter? 1177 genes is nearly 6% of our genome. 300 is about 1.5%. Those numbers are not something to trifle with, given that our reported base pair difference with chimps is about 1.3%.

Some researchers argue that the discrepancy in number is due to pruning of the data. Identifying these novel genes relies heavily on computer analysis of the human genome, and depends entirely on the assumptions made and methods used by the researchers. Some of it may be due to the same kind of bias we saw with ENCODE, the unwillingness to ascribe function to transcriptionally active non-coding DNA. Some of it may be due to reluctance to admit there are so many de novo genes, and a wish to ascribe them to junk. Some of it is definitely due to the way a gene is defined. The databases now annotate DNA as a gene if it has a homologous sequence (a sequence also present in another organism), which is precisely what novel genes do not have. One group described the problem thus,

“A serious limitation in this approach is that it relies on existing gene lists that have been annotated using criteria that usually include the presence of a homolog in other genomes. Novel genes fail to meet this criterion by definition, thus they are usually not reliably annotated. Wu et al.’s study [15] highlights the volatility of the annotation of putatively novel genes— over half of the candidate de novo genes they identified are not included in the more recent Ensembl gene lists they used (version 56), and by version 60 only six of these genes were still listed. ”

How important are these new genes? Some are associated with human disease, thus indicating their functional importance. Many of them may be used to regulate the expression of other genes. In fact, many of these genes are expressed in the developing human brain, specifically the neo-cortex, where rational thought comes from.  Many may also function in the testes. (Don’t ask me why. There appear to be a large number of new genes in other species’ testes too).

In other organisms similar stretches of DNA are non-functional, whereas in our genomes they are transcribed and in many cases, translated into protein. They lack similarity in sequence to other coding genes anywhere in the catalog of all known protein-coding genes. Because they have no relatives in other genomes, they are called orphan genes. As such, they present a strong challenge to the Darwinian story, because in Darwinian terms to be repurposed, as these genes appear to have been, requires gaining some means of turning on transcription and translation and acquiring a useful function. In fact, until about 10 years ago, everyone thought that evolving a new gene would be difficult if not impossible. Yet now we see them in every new genome that is sequenced, representing on average about 10% of that genome. Many of these orphan genes play important roles in their respective organisms. Indeed, as I said before, many of our new genes are involved in the developing fetal brain, in the neo-cortex, the part of us that distinguishes us most clearly from chimps.

It’s not something borrowed from other organisms, it’s something new that may contribute to making us who we are.

image from https://e2geneticswikid.wikispaces.com/DNA+Vocabulary

[anngauger]

The White Spaces in Evolutionary Thinking

Elegant.jpg

When certain biologists discuss the early stages of life there is a tendency to think too vaguely. They see a biological wonder before them and they tell a story about how it might have come to be. They may even draw a picture to explain what they mean. Indeed, the story seems plausible enough, until you zoom in to look at the details. I don't mean to demean the intelligence of these biologists. It's just that it appears they haven't considered things as completely as they should. Like a cartoon drawing, the basic idea is portrayed, but there is nothing but blank space where the profound detail of biological processes should be.

Let me give an example. This week Discovery Institute released a pair of videos ("How to Build a Worm" and "Switched on Worms") featuring Fellow and philosopher of biology Paul Nelson and a lowly nematode called C. elegans. Its development is precise and intricately patterned, like a Bach fugue that splits and weaves many voices into one. The final cadence is the newly hatched larva. Not coincidentally, the videos use music by Bach throughout.

C. elegans's development is a wonder to behold, well worth sharing with the world. But there is more: the development of these lowly worms exposes a major problem with the Darwinian account of evolution.

The development of C. elegans is an end-directed process. As the videos reveal, each embryo follows a precisely choreographed developmental road map in order to get to the final goal -- the reproductive adult. None of the intermediate steps on the way to the adult will do. Each step is necessary but not sufficient by itself. Turn aside from this developmental pathway and the result is likely to be a damaged worm or a dead one. Skip some steps and the same is true. How did this process come about? We would say this goal-directedness is evidence for a designer who had the final end in mind, and arranged the proper developmental steps appropriately.

Evolutionary biologists disagree. They say this exquisitely refined developmental pathway evolved gradually, a little at a time. First there was a cell, then a eukaryotic cell, one with a nucleus, organelles, and a cytoskeleton. Then along came multicellularity -- cells living together to make an organism, with some cells set aside to make the next generation, and others free to specialize. As time went on, new digestive, muscle, nerve, and sensory cells evolved and were successfully coordinated into functioning whole organisms.

These organisms then adopted increasingly complex shapes and lifestyles (including the lifestyle of the nematode worm), and developed spicules, chitin, fur or feathers, the ability to creep or to fly, to see and to sing. All these things happened because of random genetic change and natural selection. No road map, no design was needed. How do we know this happened? Because we can find a series of animals that resemble each step in the story -- Volvox, the sea urchin embryo, the planula of jellyfish, and flatworms like planaria. We find fossils that tell the story as more hard-bodied animals came along. The genes of these animals also speak of a common history (though the relationships are disputed for the deep histories). Finally, the series progresses logically, and purely by naturalistic means.

I should add that no one thinks Volvox, sea urchins, or flatworms (etc.) actually are ancestral to C. elegans or anything else. Rather these forms represent hypothetical "intermediates" that are discussed in a general way in textbooks (this may have happened, could have been, probably was...). Actual intermediates from unicellular eukaryotes to C. elegans are nowhere to be found, though. They are long gone, if they ever existed, so no one knows what they would have looked like. Despite this, names derived from these hypotheticals are assigned to clades, all based on genetic comparisons between extant species.

There's a problem, though. The story leaves out too much. To make this clear I have drawn a cartoon version (there are other versions, of course, because nobody really knows how it happened).

A cell. That step's a doozy (top left).

Cells stick together (like sponges?).

Cells form a hollow sphere with some set aside as reproductive cells, others for swimming and taking in food (like Volvox?).

Gastrulation. Cells move inward to form distinct layers and begin to differentiate one from another (like the sea urchin embryo?).

Another big step, a planula larva with bilateral symmetry, epithelium (a sheet of cells that encloses the body), a mouth, and perhaps a gut (like the planula of jellyfish? Not shown).

Over evolutionary time some planulae develop into something with a gut, epithelial, neural, muscular, and sensory cells (shown here as something like a planarium -- a small flatworm with eyespots, nerves, epithelia, muscle, and a one-way gut). Other planulae become the animals we call jellyfish or comb jellies. Then comes the evolution of all other animal forms as documented by the fossil record. Two products are shown: C. elegans and, by way of an early chordate with a notochord and gill slits, us.

This cartoon of the evolutionary story is stripped down to its bare essentials. Does it seem oversimplified? It is. Besides the fact that no one knows what happened, in biology nothing is so simple. Imagining a series of animals in such a story does not take into account or explain what is necessary for transitions within the series to take place. Similarity, or a progression in forms, does not mean there is an undirected pathway between those things. The details of how the transitions took place must be supplied, and their reasonableness assessed.

New genes and proteins must be invented. The cytoskeleton, Hox genes, desmosomes, cell adhesion molecules, growth factors, microtubules, microfilaments, neurotransmitters, whatever it takes to get cells to stick together, form different shapes, specialize, and communicate must all come from somewhere. Regulatory proteins and RNAs must be made to control the expression in time and space of these new proteins so that they all work together with existing pathways.

In fact, in order for development to proceed in any organism, a whole cascade of coordinated genetic and biochemical events is necessary so that cells divide, change shape, migrate, and finally differentiate into many cell types, all in the right sequence at the right time and place. These cascades and the resulting cell divisions, shape changes, etc., are mutually interdependent. Interrupting one disrupts the others. In C. elegans changing one cell division can have significant effects on the fates of downstream cells, and the earlier the change, the more downstream effects there will be. Coordinated, finely tuned cascades of events that lead to functional organisms cannot be produced by chance and natural selection alone.

If all these processes happen in the right way -- the road map is followed -- the cells of C. elegans successfully divide to make a worm that swims, eats, and reproduces, helping to turn compost into soil. If other creatures follow their own roadmaps, chicks hatch and caterpillars turn into butterflies, kittens are born, and babies sleep in their mother's arms.

According to evolutionary theory there is no roadmap, no design for how we got here. But after taking a closer look and filling in the details, it becomes apparent that there is a deep, coordinated, planned order in the world, as evidenced by C. elegans's development or the development of any creature -- an order with beauty and purpose, like a Bach fugue.

There's a problem, though. The story leaves out too much. To make this clear I have drawn a cartoon version (there are other versions, of course, because nobody really knows how it happened).

A cell. That step's a doozy (top left).

Cells stick together (like sponges?).

Cells form a hollow sphere with some set aside as reproductive cells, others for swimming and taking in food (like Volvox?).

Gastrulation. Cells move inward to form distinct layers and begin to differentiate one from another (like the sea urchin embryo?).

Another big step, a planula larva with bilateral symmetry, epithelium (a sheet of cells that encloses the body), a mouth, and perhaps a gut (like the planula of jellyfish? Not shown).

Over evolutionary time some planulae develop into something with a gut, epithelial, neural, muscular, and sensory cells (shown here as something like a planarium -- a small flatworm with eyespots, nerves, epithelia, muscle, and a one-way gut). Other planulae become the animals we call jellyfish or comb jellies. Then comes the evolution of all other animal forms as documented by the fossil record. Two products are shown: C. elegans and, by way of an early chordate with a notochord and gill slits, us.

This cartoon of the evolutionary story is stripped down to its bare essentials. Does it seem oversimplified? It is. Besides the fact that no one knows what happened, in biology nothing is so simple. Imagining a series of animals in such a story does not take into account or explain what is necessary for transitions within the series to take place. Similarity, or a progression in forms, does not mean there is an undirected pathway between those things. The details of how the transitions took place must be supplied, and their reasonableness assessed.

New genes and proteins must be invented. The cytoskeleton, Hox genes, desmosomes, cell adhesion molecules, growth factors, microtubules, microfilaments, neurotransmitters, whatever it takes to get cells to stick together, form different shapes, specialize, and communicate must all come from somewhere. Regulatory proteins and RNAs must be made to control the expression in time and space of these new proteins so that they all work together with existing pathways.

In fact, in order for development to proceed in any organism, a whole cascade of coordinated genetic and biochemical events is necessary so that cells divide, change shape, migrate, and finally differentiate into many cell types, all in the right sequence at the right time and place. These cascades and the resulting cell divisions, shape changes, etc., are mutually interdependent. Interrupting one disrupts the others. In C. elegans changing one cell division can have significant effects on the fates of downstream cells, and the earlier the change, the more downstream effects there will be. Coordinated, finely tuned cascades of events that lead to functional organisms cannot be produced by chance and natural selection alone.

If all these processes happen in the right way -- the road map is followed -- the cells of C. elegans successfully divide to make a worm that swims, eats, and reproduces, helping to turn compost into soil. If other creatures follow their own roadmaps, chicks hatch and caterpillars turn into butterflies, kittens are born, and babies sleep in their mother's arms.

According to evolutionary theory there is no roadmap, no design for how we got here. But after taking a closer look and filling in the details, it becomes apparent that there is a deep, coordinated, planned order in the world, as evidenced by C. elegans's development or the development of any creature -- an order with beauty and purpose, like a Bach fugue.

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Scott Gilbert’s Developmental Biology is a standard textbook used in college courses everywhere. A beautiful book with great illustrations and clear synopses of classic experiments, it provides an overall summary of what is known about how organisms develop. Yet Gilbert says on page 46...

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a

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What does it take to build an animal? Here are the job specifications. A single large cell front-loaded with information and enough energy to finish the job must be able to build an organism made of many diverse parts that all function together to solve the problems of getting resources,...

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This is cool, even if I do say so myself!

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How to Build a Worm

See the article “The Elegance of C. elegans:Classic Design in Miniature” below.

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Switched On Worms: 

The Elegance of C. elegans: Classic Design in Miniature

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When certain biologists discuss the early stages of life there is a tendency to think too vaguely. They see a biological wonder before them and they tell a story about how it might have come to be. They may even draw a picture to explain what they mean. Indeed, the story seems plausible...

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Check it out!

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DNA packaged into sub-compartments, domains and loops

Studying the design of life

We knew organization had to be a feature of DNA in the nucleus, but now we have a fine scale picture of exactly how organized it is.

For a really great video that explains it all go tohttp://www.the-scientist.com/?articles.view/articleNo/41653/title/DNA-Loop-the-Loops/

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Playing Roulette with Life

Image by Ralf Roletschek  CC BY-SA 3.0©

I’m not a person who enjoys roulette. That’s because over the long haul the house always wins. I don’t believe enough in luck to want to gamble on placing just the right bet.

Yet it seems some scientists think an incredible string of luck, analogous to making a series of very lucky bets, is the explanation for why we are here.

Here’s what I mean. In a paper just published in Nature, “Historical contingency and its biophysical basis in glucocorticoid receptor evolution,” Michael Harms and Joseph Thornton described creating an “ancestral” form of a steroid binding protein, and then testing thousands of evolutionary paths forward from the ancestral form to the present day protein. They found that two “extremely rare” mutations were absolutely required, that is, they had to be in place before the protein could ever evolve the ability to bind cortisol. Yet these two specific mutations had no beneficial effect on the protein by themselves, and so had to appear by chance!

Tracing these alternative evolutionary paths, the researchers discovered that the protein - the cellular receptor for the stress hormone cortisol - could not have evolved its modern-day function unless two extremely unlikely mutations happened to evolve first. These “permissive” mutations had no effect on the protein’s function, but without them the protein could not tolerate the later mutations that caused it to evolve its sensitivity to cortisol. In screening thousands of alternative histories, the researchers found no alternative permissive mutations that could have allowed the protein’s modern-day form to evolve. [Emphasis added.]

The above is taken from a news item from the University of Chicago Medical Center titled: “Evolution depends on rare chance events, ‘molecular time travel’ experiments show.”

It continues:

"This very important protein exists only because of a twist of fate," said study senior author Joe Thornton, PhD, professor of ecology & evolution and human genetics at the University of Chicago. "If our results are general — and we think they probably are — then many of our body’s systems work as they do because of very unlikely chance events that happened in our deep evolutionary past," he added.

What Thornton’s saying, I think, is that many mutations had to happen, with no help from natural selection, in order to make other mutations possible. And all these mutations somehow came together to make the proteins necessary to build functioning organisms. In other words, we were incredibly lucky.

Design is the better explanation, though. Think of it this way. When playing roulette, if you are looking for a specific number (mutation), you may have to wait a very long time to win your bet. You could then try again for another win, but you’d probably have to spin a long, long time to get the next winning bet. In fact, if you did keep on winning, spin after spin, everyone would wonder how you were cheating. Repeated bucking of the odds is always a sign of intelligent agency. Just ask the casinos.

Would it help to have millions of roulette tables, to continue the metaphor, all spinning at the same time to increase your chances at winning? Perhaps, but in biology, it’s not enough to have the lucky neutral mutation(s) arrive. Things get lost more often than they last. Also, eventually all those scattered winnings from different tables have to be in one person’s pocket. All the various permissive mutations have to come together in one organism.

That might sound trivial if everything was linear and tidy, like repeated spins of a roulette table, but evolution is anything but. Multiple incipient adaptive traits are being sampled all at once, each composed of various mutations, none of them beneficial yet. We have to abandon the roulette image here because it’s too simple, too linear. Evolution is more like a vast sea of unrealized possibilities with someone dipping in a ladle and pulling out a sample to drop into the next sea. Getting a workable combination by chance is unlikely to say the least.

The odds are against it. I’m betting on design.

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The Workhorse of the Cell: Kinesin

From Discovery Institute, this video gives an animated view of some of kinesin’s characteristics. You can find more about kinesin at: 

http://www.evolutionnews.org/2014/05/a_stunning_new085561.html.

Other fascinating molecular machines to follow.

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The Cell's Postal System

United States Postal Service Truck by Alexander Marks; Public Domain

The manufacturing system of cells is elegantly designed to produce proteins and other complex molecules, which must then get to the right locations. Small cells like bacteria can probably do it by diffusion, but larger eukaryotic cells need a directed delivery system. As a result, eukaryotes have efficient motors to carry cargo, and a “postal system” to direct the motors to the appropriate destinations.

Destinations differ. Some cargos go to the growing front end of a migrating cell. Others must travel the length of a neuron’s long axon to get to their destination. And some have to be exported outside the cell. As an example, epithelial cells have three distinct surfaces, top, bottom, and sides. Each surface needs a different set of molecules delivered to it. Without this differentiation, tissues and organs made of epithelial sheets could not form or function properly,

In embryos, special “determinants”, either protein or RNA, have to be delivered to the right location in the developing egg or embryo. Once again, without these determinants the body plan of the nascent embryo is disturbed.

How is all this coordinated? How does the cell know where to deliver its products? What is the address system? Where precisely is the map that matches all these addresses? And who is the postman that matches address to map and delivers the package to the right address?

There are three “postmen,” dynein, kinesin, and myosin. For delivery to the periphery of the cell, the job is usually done by kinesin. Kinesin is composed of two parts— two heavy chains that form the walking two-headed motor and its long coiled stalk, and two light chains, that bind at the end of the stalk and make a fan-like tail.

Illustration by Vladamir Shirinsky http://eng.thesaurus.rusnano.com/wiki/article945

It has long been thought that the light chains are involved in binding to and perhaps distinguishing among the many cargos that kinesin delivers. It is also thought they play a regulatory role for the motor domain. If the kinesin heavy chains have no attached light chain, they fold on themselves and inactivate the motor. So the light chains function like an on-off switch for the motor, which helps to conserve energy. They may also serve to promote interaction and cooperation between dynein and kinesin.

There are multiple versions of the light and heavy chains. Some are generalists, and some are specific to particular cell types. We now know that defects in different kinds of heavy and light chains are associated with particular diseases, most notably, Alzheimer’s.

What we do not know is how everything gets sorted to the right destination. There is much more work to be done, but progress is being made in determining some of the linking ”address” proteins that bind the light chains.

This system is present in most if not all eukaryotes. In fact, it appears to date back to the first eukaryotes. Let’s consider how this system might have come about. All parts are necessary for it to work. To return to our metaphor, if the postman just started transporting things at random, what benefit would that be? Yet address molecules are of no use without a postman, or without paths to travel on. Thus directed transport requires a complicated set of interacting parts, each of which is essential.

Without these motors and their interacting proteins, migrating cells wouldn’t have the materials they need to move forward. Axons would die from lack of mitochondria and/or they would send signals very inefficiently. Epithelial cells would have their bottoms and tops confused. And embryos? A mess. 

Oh, and I haven’t mentioned that both kinesin and dynein are essential for chromosome movement and spindle formation during cell division.

 Amazing. Hard to sort out how it happened, isn’t it?

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Intelligent Design Research: BIO-Complexity 2013

The most recent article published in BIO-Complexity considers the wild and abstruse world of metabiology, a theoretical computational attempt to model evolutionary biology. Dr. Gregory Chaitin began the work in 2009, and it has progressed to the point described in his 2012 book Proving Darwin, shown below. The question is, does his model succeed?

Winston Ewert, William Dembski and Robert Marks II take on that question in their article in BIO-Complexity, whose abstract is below. I will let them speak for themselves.

Active Information in Metabiology Winston Ewert, William A. Dembski, Robert J. Marks II

Abstract

Metabiology is a fascinating intellectual romp in the surreal world of the mathematics of algorithmic information theory. In this world, halting oracles hunt for busy beaver numbers and busy beaver numbers unearth Chaitin’s number, knowledge of which in turn allows resolution of numerous unsolved mathematical problems, many of whose solutions would earn large cash bounties. All this, despite the fact that halting oracles can’t be implemented on a computer, a computer can never make a list of busy beaver numbers, and Chaitin’s number, always a positive real number less than one, is proven to be unknowable. The fun of metabiology is the application of these ideas to illustrate Darwinian evolution. When metabiology’s evolutionary process is stripped of the glitter of algorithmic information theory, however, what remains is a procedure similar to that used in other attempts to model Darwinian evolution, like the ev and AVIDA computer programs. Metabiology, like ev and AVIDA, succeeds because available sources of knowledge about the solution being sought can be mined. We show the mining of information from a halting oracle has striking similarities to mining information from a simple Hamming oracle. Unlike a halting oracle, however, Hamming oracles can be implemented on a computer. We demonstrate that for both oracles, information can be mined by search strategies that are analogous in some respects even though the methods differ; in both cases the search strategy used greatly influences the result. Because metabiology’s process relies on unknowable numbers and infinite resources, its reported relative performance measures can only be expressed asymptotically. That is, the results of metabiology are only proven to be true on the largest possible scale. In fact, simple simulations using bounded resources suggest the asymptote is not always approached quickly, indicating that metabiology results may only hold for scales larger than any practical system.

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Celebrate our 100th post!

Photo by Shannon Kringen, Wikimedia commons

This last week we posted our hundredth post. It took us until Friday the 13th under a full moon with massive solar flares to notice. Just kidding! But we are a little dizzy.

You are invited to check out the archives to find your favorite.

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Kinesin: Fast, Efficient, Essential, and Mysterious

Perhaps you’ve seen the video from Discovery Institute of the miniature walking machine known as kinesin. This microscopic marvel helps to get the cell’s protein products distributed to their final destinations, among other things.

Kinesin’s movement is extremely efficient, and by itself is a wonder. But there’s another wonder. A single kinesin can pull its cargo at up to 800 nanometers per second along its microtubule highway, depending on its load and the amount of ATP available. That’s almost a micron per second. To give you a sense of scale, one bacterium is about a micron in length, and a typical animal cell is roughly 10 microns. That means that, under optimal conditions, and if kinesin is unobstructed, it could travel the length of an average cell in about 12.5 seconds. That is fast. If it partners with other kinesin molecules, it can move even faster.

This is a good thing for our neurons. A neuron has its nucleus and  biosynthetic apparatus in its cell body. This where  the proteins and organelles that the neuron needs are made. But these proteins and organelles are used out at the very tip of a long thin process called an axon, which extends from the body of the neuron all the way to the place it sends its signals.

Different kinds of neurons. Image by Jonathan Haas via Wikimedia Commons

In the brain there are billions of neurons with axons connecting  one region to another (the different kinds are shown above). In the peripheral nervous system, axonal processes can reach up to several feet in length. For nerves running to your toes, for example, axons must reach all the way from your lumbar spine. Therefore anything delivering essential items down axons needs to be fast. 

How do the proteins and organelles get from where they are made to where they are used? And how do things that need to be recycled return to the cell body? It’s by means of kinesin for outward bound travel and another motor protein called dynein for inward bound travel. Remarkably,  dynein and kinesin cooperate, rather than compete—otherwise there would be a constant tug of war in the cell. They “know” where packages are meant to go, and which motor protein should do the job. How that happens is a whole other story. 

This isn’t just abstract stuff. Many neurodegenerative diseases have been linked to mutations of kinesin, including Alzheimer’s disease. So this little workhorse of the cell is not only a marvel, but essential.

If you’d like to see a short time-lapse video of axonal transport in hippocampal neurons, click here. 

Finally, in order for kinesin to do its work, we need the motor protein itself, the microtubule highway it walks along, and some mysterious means of connecting and directing where its cargos get carried. This whole system appears to be essential for a variety of eukaryotic cell functions; at least eleven kinesin families appear to have existed in the putative last common ancestor for all eukaryotes. Yet evidence for kinesin motor proteins in bacteria is sketchy at best. Thus we have another complex system necessary for eukaryotic cellular function that seems to have appeared out of nowhere.