Biologic
Perspectives

A Pretty Sharp Edge: Reflecting on Michael Behe’s Vindication

By Ann Gauger

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I am writing a post that shouldn’t have to be written. It’s about Dr. Michael Behe’s book The Edge of Evolution, what it predicted, how that prediction was confirmed, and how his detractors continue to quibble and obfuscate, claiming that even if he was right he was still somehow wrong. That’s not the way scientists are supposed to operate.

In science, theory that explains data and makes a prediction that is experimentally verified is considered to be confirmed. That’s the way it is supposed to work. Einstein’s general theory of relativity, Mendeleev’s periodic table, and many other theories have been verified this way.

Now let’s look at Behe’s theory. Malaria is a devastating disease caused by the parasite P. falciparum. These parasites are quick to develop resistance to most drugs, but they have had a hard time overcoming chloroquine, requiring more than ten years to develop resistance. In fact, sixty years since the drug’s introduction, and after more than 10^20 malarial parasites total, resistance to chloroquine has developed fewer than ten times. Why?

In The Edge of Evolution, Behe proposed an answer. His explanation — his hypothesis, if you will — is simple. The mutation rate of P. falciparum is roughly 1 in 10^8 mutations per base pair per parasite. There are on average 10^12 parasites in the human body — that’s enough for more than a thousand copies of every possible single mutation to exist somewhere in each infected person. So if resistance required only one mutation, it should have appeared in a few days. However, it took more than a decade for resistance to emerge. Behe argued that therefore at least two mutations must be required for the parasite to develop resistance to chloroquine. Furthermore, those two mutations must each be of no use as single mutations, andthose two mutations must be present together in the same organism in order to confer resistance to the drug.

Why did Behe make these predictions? It’s a simple calculation, really. If two simultaneous mutations are required for resistance, the rate of that double mutation occurring can be calculated by multiplying the single rates together. That makes the rate for two mutations roughly 1 in 10^16 mutations per base pair per parasite. To find those two mutations would require many more trials than are available among the 10^12 parasites in each person infected. However, 10^20 parasites (the total present in a single year) represent more than enough opportunity for that double mutation to occur.

His critics focus on Behe’s use of the word “simultaneous.” Getting two simultaneous mutations is ridiculous, they say, and so multiplying two rates together is ridiculous. 

Maybe the two mutations happened simultaneously, meaning together in the same molecule in one generation. It is possible. Maybe the mutations happened one at a time. We don’t know. Parasites carrying single mutations on the path to resistance (meaning they have no resistance yet) are sickly, though, because those single mutations have damaged an essential function. They and their offspring might survive and reproduce long enough for a second mutation to occur, but it seems unlikely. Most of the time they will simply be out-competed by their non-mutant siblings.

Another critique Behe’s opponents offer is that Behe just doesn’t understand evolution. There must be some cumulative adaptive path that would take the parasite to drug resistance. In support they offer Joe Thornton’s work with hormone receptors, where his lab evolved a hormone receptor from its “ancestral” form by a series of selective steps. Thus there can’t be an edge to evolution as sharp as just two mutations, they say. What the critics don’t say is that the first step is not a selectable step. It’s a gully across the road to new function that must be crossed by jumping.

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The same is true about the path to chloroquine resistance. First of all, common sense says if there were a selective path with each mutation conferring increasing resistance, it would happen quickly, much more quickly than in a decade. But more importantly, a recent paper by Summers et al. has shown by experiment that two mutations, neither of them conferring any resistance by themselves, are the first steps of chloroquine resistance. (One mutation is required by all pathways; then either of two other mutations can be used to bring about resistance.) This is a more like a canyon than a gully. Two mutations must be present together in the same molecule to confer resistance to chloroquine. Call it “occurring simultaneously” or not. The effect is the same, and Behe is right and his critics are wrong. 

Ironically, recent work has shown the same thing with regard to hormone receptors. Carroll et al. (2011) reported that at the base of the pathway to evolve the ancient hormone receptor there are two mutations (a gene duplication plus point mutation) that must occur before any further evolution is possible. Harms and Thornton then showed that these mutations are the only way forward. There is no other road to take, no way around the canyon. It sounds remarkably like the malarial resistance pathway, doesn’t it?

So how sharp is the edge of evolution? For the malarial parasite P. falciparum, the edge of evolution for chloroquine resistance is two mutations: one specific mutation and either one of two other mutations.These mutations have to occur together, and they have to be there before any other mutations can have any effect. If the parasite doesn’t have these two mutations, it remains chloroquine-sensitive. But as we have seen, getting two mutations can take a long time. It happens relatively quickly for malaria because of its huge population size. For us and other animals it may take an extremely long time.

That sounds like a pretty sharp edge of evolution to me.

Behe predicted this requirement for two mutations seven years ago. All continuing criticism now sounds like sniping and quibbling over terminology. Maybe those quibbling and sniping can’t see they are wrong. Maybe they don’t understand how science works and what counts as evidence. Or, and this is more likely, they will never admit that Behe is right and they are wrong.

Photo credits: LeHigh University and Flickr

Two of our favorite animations from WEHI. First, what it takes for chromosomes to condense, and we mean really *condense.* Second, the process of copying DNA. If you thought it was simple, look again. It’s like sewing and fly fishing put together, but on nanometer scale. 

On Human Origins, A Cautionary Tale With "Surprising" Biological Results

By Ann Gauger

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This post is a follow-on to the previous postWhy Does Biology Still Have the Ability to Surprise Us?

Back in the late 1980s and early 1990s, DNA sequencing was sweeping the scientific scene because of its power to answer a number of unsolved problems. 

 Cann et al sequenced mitochondrial DNA from around the world to show that all women were descended from a single woman who lived some time around 200,000 years ago. (Similar work was also done for the Y chromosome and the male lineage.) One of the possible interpretations of this study was that the single woman was Eve.

The scientist Francisco Ayala did not like this interpretation. To do him justice, it is indeed possible that there were many women alive at the time of the woman progenitor “Eve”, and that their lineages died out over time. Nontheless, Ayala set out to to not merely challenge but to disprove even the possibility of an historical Eve (and Adam), using the same sequencing and phylogenetic analysis methods that Cann et al had used. For his study he chose to analyze a highly variable gene, HLA-DRB1, that is part of our immune system.

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HLA-DRB1 is located in the the human leukocyte antigen (HLA) complex. Most of the genes that encode the proteins involved in immune defense are located here. Some of these genes are highly variable in sequence, with hundreds of alleles each, including HLA-DRB1.

The variation of HLA-DRB1is mostly limited to one small domain of the protein, called the peptide binding site (PBS). The PBS is where the rubber meets the road for recognizing and presenting foreign proteins to the immune system. Variation in the PBS increases the chance that at least some individuals in the population will survive a new parasite or disease;  one of these proteins may have a PBS with the right sequence to bind proteins from the attacker. That HLA protein can then  direct the immune system to search and destroy anything carrying those foreign proteins.

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Ayala sequenced the DNA encoding the PBS of HLA-DRB1 precisely because this gene has hundreds of variants in the current population. He compared DNA from many Rhesus macaques, chimpanzees, and humans, and based on those sequences, he constructed a phylogenetic tree—a tree intended to show the evolutionary history of this gene.

His conclusion? To account for the genetic diversity, there had to be at least thirty-two separate lineages of the gene at the time chimps and humans  diverged from each other. And he explicitly argued that this ruled out a single Y-chromosome Adam and mitochondrial Eve.. as our original progenitors

But this wasn’t the end of the story. A few years later another group headed by Tomas Bergström challenged Ayala’s work, saying that he chose the wrong piece of DNA to study. The PBS sequence was inappropriate because it suffered from a high mutation rate and a high rate of gene conversion, both of which would cause an overestimation of the number of lineages for this gene.

Bergström’s group  sequenced a neighboring region of the same gene that should not have these problems. They found that the estimated number of HLA-DRB1 lineages dropped from thirty-two to seven.

Now here’s where it gets interesting. The same group later sequenced a number of individual  HLA-DRB1 genes again, but this time they sequenced the whole gene, a monumental task given its size. Guess what they found? Only four lineages predate the split of chimps and humans. A fifth arose about 3-5 million years ago.

Sequencing the whole gene from many individuals gave them more complete data, and permitted a finer resolution of the sequence comparisons. It also revealed a number of very interesting things. The introns (the non-coding portions of the gene that get spliced out before it is turned into protein) showed that the four lineages appeared to have been separate for a long time, based on the differences between them. It also showed that there had been an explosion of genetic diversity about 500 to 350 thousand years ago. It was about that time we went from a few lineages of HLA-DRB1 to many, resulting in the incredible diversity we see today.

Let me restate this in case you have missed it. Four lineages of this gene appear to be ancient, because they are so different from one another. But derived from each of those lineages are many, many alleles produced by some process that generates diversity fast, These newly appearing lineages tend to be more similar to one another, indicating that they are young. Surprisingly (there’s that word), their diversity appears to have arisen less than half a million years ago. This result has challenged the strongly held views of some immunologists, and is causing a re-evaluation of the field.

Here are a few  take-home lessons:

1. Scientists would be wise not to make strong claims on incomplete data.

2. Science does tend to be self-correcting in the long run.

3. The diversity of the human HLA complex is not due to the ancient preservation of many lineages. Rather, most of the variation is recent, and comes from only four lineages. 

4. From thirty-two to seven to four. That’s a remarkable journey, one that was entirely unexpected (there’s another of those words). Four alleles can be carried by just two individuals. 

Ayala’s conclusions were premature to say the least, and his argument against Adam and Eve has now been dismantled. In addition, the new evidence  has indicated there must be a new explanation for HLA complex diversity. 

As to the reality of Adam and Eve, I leave you to draw your own conclusions. But don’t be hasty. There’s a whole genome yet to explore.

Photo credits: Paul Maximus/Flickr

Why Does Biology Still Have the Ability to Surprise Us?

By Ann Gauger

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About forty years ago, a biochemistry professor told my class that now that the genetic code had been worked out and the lac operon discovered, the only thing left for us students was to work out the details. Boy, was he wrong!

If there’s one thing I’ve learned over the last forty years, it is that every ten years or so the biological apple cart is upset, and a long-established “fact,” an assumption based on incomplete knowledge, is proven to be wrong.

I am sure you can find textbooks that still include some of these old “facts.” Below is a partial list of the “facts” that have had to be revised, and some that are still under discussion.

1. Old fact: DNA is stable and genes don’t hop around.

New discovery: Mobile genetic elements can hop from place to place in the DNA, duplicating themselves and changing gene expression. Sometimes they carry surrounding genes with them.

2. New “old” fact: Mobile genetic elements are selfish DNA that replicate themselves without benefit to the organism, thus cluttering the genome with garbage.

New discovery: Mobile genetic elements appear to be involved in the regulation of many important genes, and their distribution in the genome is nonrandom.

3. Old fact: A gene is an uninterrupted stretch of DNA that encodes a single protein. Genes are arranged like beads on a string.

New discovery: Genes in eukaryotes are interrupted, sometimes multiple times, by non-coding sequences called introns. The introns get spliced out of the messenger RNA before the message is translated. Because of splicing, one gene can produce many different but related proteins.

New discovery: Genes can overlap one another on the same stretch of DNA, on the same strand or on opposite strands. Thus one piece of DNA can produce multiple different proteins.

Take home message: 1 stretch of DNA ≠ 1 gene ≠ 1 protein

4. Old fact: There are only 3 forms of RNA: messenger RNA, transfer RNA, and ribosomal RNA.

New discovery: New classes of short and long RNA transcripts serve to regulate gene expression.

5. Old fact: Pseudogenes are useless broken remnants of former genes.

New discovery: Not all pseudogenes are useless. Pseudogenes can be transcribed, and their products can be used to regulate the expression of their full-length sister genes. Related to #4.

6. Old fact: The genome is full of junk, the remnants of wasteful evolutionary processes and selfish DNA (see #1, #2 and #5 above).

New discovery:  ”Junk” DNA isn’t junk after all. It has many important regulatory functions in the cell.

Revolutionary discoveries like these often happen when someone tries something new, stumbles across some contrary evidence, and begins to question the validity of an established “fact.” The results have been astonishing—and have even won the Nobel Prize. Because of these discoveries we have gained a new and better, though still imperfect understanding of biology

Why should we still have the “facts” wrong? After all, we’ve been studying biology for 60 years after the discovery of DNA’s structure, and 50 years after the code was worked out.

Perhaps a better question would be, “Why does biology have the ability to surprise us?” It’s because life is much more sophisticated than anything we can imagine. We look at biology from our very limited perspective, and at almost every turn we are puzzled or amazed. You can even read it in the understated, carefully couched language of published articles, where words like “surprising” or “unexpected” appear often.

Remember that biochemistry professor who claimed that all the important work in biology was done? He also said we’d never find gears or wheels in biology. Poor guy!

You’d think that scientists would be more cautious about our pronouncements if we can be so wrong. But we are only human, like everyone else, and our accepted “facts” are often deeply entrenched in our thinking. In truth, though, only one rock solid “fact” exists—that some time in the not too distant future a strongly held “fact” will be proven mistaken.

Like neo-Darwinian evolution, perhaps?

Image credit: National Geographic

Playing Roulette with Life

By Ann Gauger

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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.

The Cell's Postal System

By Ann Gauger

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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.

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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?

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.

Celebrate our 100th post!

By Ann Gauger

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.