Gene Therapy for Mouse Vision

This version of the article differs slightly from the Without Apology version.

By Michael Hawkins

Gene therapy is generally a good thing. Just last year it was used to cure color blindness in spider monkeys. In that instance, an adeno-virus was used to deliver the correct gene into the primates; that’s often how it is done. However, there are drawbacks to this. For instance, insertional mutagenesis may occur. This is where an inserted sequence causes a change in the expression of a nearby gene. In many cases, this will cause cancer. It doesn’t always happen and not all viruses will be the right kind to integrate themselves into the host’s genome, but the possibility is a very real one. Fortunately for the spider monkeys, no side effects have been noted.

Another way to go about fixing faulty genes is to do what Cai et al. did and deliver the correct DNA via nanoparticles. They injected mice which had retinitis pigmentosa, a disease of the eye, with saline, naked plasmid DNA (i.e., not compacted in a nanoparticle), and with nanoparticle compacted DNA (plus a control group that received nothing). The correct gene, the Rds gene, did nothing when it was given alone (and, of course, the saline did just the same). However, the nanoparticle DNA did prove to have an effect. In fact, not only did it retard further degeneration of vision, but it even caused healing in the form of functional and structural improvements.

There are still safety issues that need to be fleshed out with more research, but this method of correcting faulty genes is both promising and pretty exciting. What’s more, it even has opened the avenue for some good zingers.

“Making the blind see was once called a miracle,” said Gerald Weissmann, M.D., Editor-in-Chief of The FASEB Journal. “As we have expanded our understanding of evolution, genetics, and nanotechnology, chances are that “miraculous” cures will become as commonplace as those claimed by faith-healers past and present.”

1. X. Cai, S. M. Conley, Z. Nash, S. J. Fliesler, M. J. Cooper, M. I. Naash. Gene delivery to mitotic and postmitotic photoreceptors via compacted DNA nanoparticles results in improved phenotype in a mouse model of retinitis pigmentosa. The FASEB Journal, 2009; DOI: 10.1096/fj.09-139147

Mitochondria and Microsatellites

By Michael Hawkins

Mitochondrial DNA (mtDNA) is useful for determining the phylogeny, or relationships, between closely related species. It is inherited, generally, only from mother to offspring, so it doesn’t face problems such as recombination since it isn’t recombining with other DNA before being passed on (except through horizontal transfer, or “genetic swapping” between bacteria).

One recent discovery using mtDNA has found that a sort of “pre-human” was walking around while humans and Neanderthals were still rocking out. Johannes Krause of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany and his colleagues wrote in the journal Nature that they had sequenced mtDNA from a fossil discovered in a Siberian cave. Results showed that the former owner of those long dead bones had diverged from humans and Neanderthals a million years ago. (Human and Neanderthals then diverged 500,000 years later.)

The authors go on to state that more research is needed to determine just where the species qualitatively sits on the evolutionary tree. The point, however, is that mtDNA has proved useful in this analysis, giving a tentative quantitative determination and a tentative qualitative indication.

This is all in stark contrast to microsatellites. These are short tandem repeats, or units of repeating DNA sequences. For example, CACACACACACACACACACA is commonly seen throughout eukaryotes and the chloroplastic genomes of plants (usually every few thousand base pairs). They are generally neutral.

Microsatellites have relatively high mutational rates for a variety of reasons. Whereas in mitochondria the mutational rate can partially be chalked up to the fact that mitochondria is bacterial in origin, microsatellites have polymerase slippage to thank, or bad DNA replication, let’s say. Other studies suggest unequal crossing-over. At any rate, this mutation rate lends itself to population studies using microsatellites.

By using microsatellites as genetic markers, it is possible to determine genetic variation within a population. This works for investigating both temporal and spatial population structure, two important factors in management and conservation of species. For instance, Lage et al. 2004 looked at Atlantic cod populations ranging across Browns Bank, Georges Bank, and Nantucket Shoals.

At the time of the research, the Gulf of Maine cod were treated as a separate stock from the Nantucket Shoals and Georges Bank Atlantic cod. Browns Bank cod were even more separate as a stock since they are in Canadian waters. Using microsatellites, the researchers found Nantucket Shoals cod to have a distinct population structure from those on Georges Bank and Browns Bank, which were genetically similar. One likely reason is due to currents which keep Georges Bank cod on Georges Bank as well as somewhat rare currents which likely transport larvae from Browns Bank over the Fundian Channel (which adult cod are unlikely to traverse since they are ground-huggers and the channel is deep and cold). The conclusion is that the health of Atlantic cod populations might be better served by treating them as separate stocks based upon the discovered genetic variation, instead of the current method of utilizing particular geographical lines which may not reflect all population ‘barriers’.

The shortcoming, however, with microsatellites is that they are not useful for deep phylogenetic analysis. Their high mutation rate makes them virtually useless after a few thousand generations; they are good for pedigrees and population structure analysis, but they do not offer insights into distant relationships. Occasionally they may remain the same or nearly the same over long periods of time, but the rhyme and reason probably has nothing to do with the microsatellites themselves. Instead, they likely are located near a site of selection on a locus, thus conserving them for longer than just those few thousand generations.

Lage CR, Kuhn K, Kornfield I. (2004) Genetic differentiation among Atlantic cod (Gadus morhua) from Browns Bank, Georges Bank, and Nantucket Shoals. Fishery Bulletin, 102:289-297.

Oh, How Times Have Changed

By Michael Hawkins

In all my attempts to explain certain things about science, I’ve noticed something: a lot of people just don’t know the general timeline of significant events. These are important things to know, if only so one can at least have a general idea of what’s going on whenever science is discussed. Even more to the point, I would have to imagine a lot of people care where their money is spent. In Europe, for instance, one of the largest scientific collaborations amongst nations, the Large Hadron Collider, has a budget of roughly 9 billion dollars. Most of that is not American money, but regardless, the people who are paying for it ought to know that it is entirely predicated on the notion that the Universe emerged from the Big Bang roughly 13.7 billion years ago. If someone believes instead that the Universe is, say, 6,000 years old, then there is clearly an issue. The predication on which the Large Hadron Collider stands doesn’t make much sense for that person.

So it is with that in mind that I present my own attempt to knock down that sort of ignorance, or at least give a refresher. “BYA” stands for “billion years ago”, with the substitute “M” meaning “million”, and “T” standing in for “thousand”.

13.7 bya – Big Bang
13.0 bya – First galaxies form
10.0 bya – Milky Way forms
4.6 bya – The Sun forms
4.5 bya – Earth forms
3.9 bya – First life appears
3.0 bya – Photosynthesis appears
2.1 bya – Eukaryotic cells appear (you are a eukaryote)
1.0 bya – Multicellular life appears
580 mya – Cambrian explosion, tons of complex arms races evolve
400 mya – Tetrapods evolve
360 mya – Amphibians evolve
230 mya – Dinosaurs evolve
200 mya – Mammals evolve
150 mya – Birds evolve (we would have called them dinosaurs at the time)
65 mya – Big ol’ asteroid. Dinosaurs that can’t fly die out
50 mya – With T-Rex et al gone, mammals diversify
5-7 mya – Great apes, monkeys split (humans are great apes)
2.6 mya – Earliest tool use detected
150 tya – First anatomically apparent humans emerge
30 tya – Last Neanderthals die
15 tya – Wolves domesticated as dogs
11 tya – End of last ice age
5 tya – First preserved written language
3 tya – Egyptians build pyramids. Also praise cats.
476 AD – Fall of Rome
1643 – Newton is born
1743 – Thomas Jefferson is born
1809 – Charles Darwin and Abraham Lincoln are born (same day)
1999 – Mystery Science Theater 3000 is cancelled
2009 – See evening news

So there you have it. A basic sketch of what has happened over the past 13.7 billion years. While most events, such as the extinction of the dinosaurs 65 million years ago, don’t tend to be as hurtful as the cancellation of Mystery Science Theater 3000, they are all important.

Finally, the point of the time line I want to really take a moment to point out is with the evolution of humans. The split between us and other modern apes occurred roughly 5-7 million years ago. Emphasis on “other”. There is no taxonomic grouping that separates humans and, say, orangutans on the Family level. Humans, orangutans, gorillas, and chimpanzees are all Great Apes. Further included in that grouping would be a massive number of extinct species, many of which would resemble early humans in a number of ways. (And by “early”, I mean humans from just 50,000-100,000 years ago.) We are apes, which are first primates which are first mammals which are first vertebrates which are first animals which are first eukaryotes which are first simple replicators which are first the stuff of stars.

Tetrapod Evolution Pushed Back 18 Million Years

By Michael Hawkins

Researchers have recently discovered fossilized tracks which push the evolution of tetrapods back by 18 million years.

The discovery from southeast Poland shows imprints with the clear outline of toes. The distance between the tracks as well as their particular pattern also offer a glimpse into the size of the animal, which is estimated to be between 6 and 7 feet long.

Tetrapods are four-footed or four-limbed vertebrates. All birds, reptiles, amphibians, dinosaurs, and mammals fall into that category.

Until recently, tetrapod fossils had been dated between 375-380 million years in age. Tiktaalik roseae, discovered and described by Neil Shubin et al in 2004 on Ellesmere Island in Canada, was one of these fossils. Shubin had actually specifically predicted he would discover Tiktaalik where he did based upon evolutionary science at the time: there were no tetrapods 390 million years ago but there were tetrapods 360 million years ago. Thus, he should find a species showing features of both fish and tetrapods somewhere between those dates. He was successful, but now his discovery needs some minor explanation in light of tetrapod evolution actually being pushed back to 397 million years ago (and probably more).

The fact is that this new discovery represents a quantitative change, not a qualitative one. That is, the relations between fish and tetrapods and the evolutionary time line laid out for them has not been altered. What has been changed is the quantity of time now evident for tetrapod evolution. It is actually not entirely surprising; Tiktaalik still represents an awesome transition between marine and land vertebrates, but it wasn’t the only creature able to drag itself out of the oceans. Shubin, in fact, had described Tiktaalik as a representative of the sort – key word, sort – of ancestor tetrapods have in his original paper. We should expect to find other tetrapods walking around in ancient times; we just didn’t know exactly how ancient those times were.

Devil Facial Tumour Disease

The seemingly needless “u” in “Tumour” is how it is written in reference to the disease, regardless of the country.

By Michael Hawkins

Devil Facial Tumour Disease is a particularly nasty cancer afflicting the Tasmanian devil population of Tasmania right now. It is spread by devils biting each other in the face and has been fatal for upwards of 50% of the population. Recent research has shed some light onto its origins.

Australian scientists found that the disease originates in Schwann cells, which protect peripheral nerve fibers. This has opened the door to the discovery of a genetic marker which can be used to diagnose the cancer.

What they also found was that in each subject, the disease was fundamentally the same. That is, the cancer does not originate in the individual devils, but instead comes from one common source, some long deceased devil. This means the disease can effectively be regarded as a separate organism, free to undergo its own evolution. Of course, its evolutionary ‘goals’ do not jive with the evolutionary ‘goals’ of its host, so there is an obvious conflict. (Please note the scare quotes around “goals”. The term is metaphorical.)

The cancer may become more and more virulent, allowing it to spread further and faster around the island. That could mean the end of both the devils and the cancer. Eventual death is not a very good long term evolutionary strategy, but then natural selection does not have any sort of foresight. Alternatively, the cancer could become less virulent so that its host could survive longer, thus offering the devil a greater chance to pass the disease along. Either way, the devils are out of luck.

One question this indirectly raises is if this susceptibility to cancer has anything to do with poor contact inhibition, the mechanism by which cells stop reproducing upon coming into contact with each other. Cells that don’t do that are called cancer. Most animals have one gene for this (p27), but naked mole rats have two (p27 and p16). This constitutes an extra barrier against cancer; as such, naked mole rats have never been observed to have developed cancer. Ever.

This means that at least one theoretical avenue of research into the cancer afflicting devils could be into the efficacy of their p27 gene: it may not offer the same effectiveness it does in other animals, especially considering the devil’s susceptibility to cancer in general.

But wherever the research should go, the dwindling Tasmanian devil population clearly needs help. And soon.

Only in the Light of Evolution

The following also appears at For the Sake of Science. Presented here is that version rather than the version for the physical copy of Without Apology.

By Michael Hawkins

We should see fossils in a certain order if evolution is correct. They should go from simple to more complex overall, and the fossils we see in the most recent strata should resemble extant life much more than the fossils we see in old strata.

We should also see changes within lineages. We should be able to observe instances of gradual change in species that eventually leads up to either current species or at least to the time of extinction for these species.

Here’s a simple timeline of life’s history. Click it.

What the evidence shows is gradual change. First we find simple bacteria which survived off energy from the Sun, then we see more complicated cells known as eukaryotes arise. (You are a eukaryote.) Next we see a slew of multi-cellular animals arise. They’re still simple, but much more complex than the original bacteria. A few million years later more complicated life arrives. Early (and simple) plants begin to take hold. Soon the fossil record begins to show more plant complexity with low-lying shrub such as ferns, then conifers, then deciduous trees, and finally flowering plants. Gradual changes occur in the oceans and fresh waters which lead to fish and then tetrapods (Tiktaalik comes to mind).

One of my favorite fossils is trilobites. They’re extremely common due to their hard bodies. In fact, even their eyes are well-preserved because of their hard mineral make-up. I personally recall entering touristy-stores seeing countless fossils of these guys in the mid-west to the west (which, unsurprisingly, was once a shallow sea). This image shows the different lineages of this organism. Studies show that the ‘rib’ count has changed over time in each individual species, often without regard to how the other species changed. Going back further, there is less and less divergence in each species. Eventually, as evolution predicts, they all meet at a common ancestor.

So naturally the next step is to find fossils which show more significant changes. Let’s take birds and reptiles. They hold similarities between each other, both morphologically (certain shapes and structures) and phylogenetically (genetic sequence). A good hypothesis is that they came from one common ancestor. If this is true, the links between birds and its ancestors and reptiles and its ancestors should lead to the same point. They do. Dinosaurs are the ancestors of both. The links between birds and dinosaurs are so incredibly well established that I’d prefer to not go over them in detail. But for starters, some dinosaurs sported feathers and claws and had the same proteins for the feather-making process as extant birds. The links between reptiles and dinosaurs is easier just on intuition, so I’ll leave it at that for now.

Other transitional fossils include the already mentioned Tiktaalik. A view of the history of life can be see here. This shows the change in head and neck structure. Recent research on long-ago discovered Tiktaalik fossils has shown the importance in the gradual bone changes in the neck. These changes – a hallmark of evolution – were important to the ability to turn its head. This is a hallmark because natural selection only modifies what already exists. This is precisely what happened.

Going further with this example, evolution makes predictions as to how early fish evolved to survive on land. If there were lobe-finned fish 390 million years ago and obviously terrestrial organisms 360 million years ago (which is what the fossil record shows), then if scientists are to find transitional fossils, they should date in between that time frame. There should be an animal that shows both features of lobe-finned fish and terrestrial animals. Tiktaalik is that animal. It has fins, scales, and gills, but it also has a flat, salamander-like head with nostrils on top of its nose. This is a good indication that it could breathe air. Its eyes were also placed there, indicating that it swam in shallow waters. Furthermore, it was lobe-finned, but shows bones (which eventually evolved into the arm bones you used to get out of bed today) that were able to support its weight to prop itself up. And of course, it dates to 375 million years ago.

Next, evolution says the fossil record should show recent fossils being more closely related to extant species than are early fossils. This is precisely what happens. Sixty million years ago there were no whales. Fossils resembling modern whales only show up 30 million years ago. So, again, evolution makes a predication: if transitional fossils are to be found, they will be within this gap. And so it is.

We begin with Indohyus. It was an artiodactyl. This is important because extant whales have vestigial bones which indicate that they came from this order: scientists expected to find this because, again, evolution predicted it. It should be of no surprise that this fossil dates to about 48 million years ago, right in the predicted gap. From here there is a gradual evolution shown in the fossil record which leads up to modern whales.

The lac Operon

This article has appeared separately at For the Sake of Science.

By Michael Hawkins

The lac operon of E. coli is the classic example for describing inducible prokaryotic gene expression. One excellent video description of it can be found here.

The jist is this. Not all genes are turned on all the time. There are ones which are needed constantly, others which are only needed in specific types of cells, and then others which are ‘turned on’ in specific situations. It is on this last point which I will focus.

In order for a gene to be ‘turned on’, it must be ‘off’ in the first place. All this means is that an organism’s (relevant) DNA is not being transcribed, thus preventing translation and the manifestation of proteins. The way this occurs in E. coli by means of the lac operon is that the lac repressor is bound to a DNA sequence.

A repressor is itself a protein. It binds to an organism’s DNA, thus preventing RNA polymerase from transcribing anything. This is a physical blockade; the repressor prevents the RNA polymerase from physically attaching and running along a specific sequence of DNA. This is the default position for an inducible repressor.

The way the repressor is removed is simple to understand. It has a specific shape to it which enables it to bind to the DNA sequence. However, this shape can be changed if lactose is present. The lactose will bind to the repressor, thus causing an allosteric change in shape. This means the repressor is no longer the specific shape needed to attach to the DNA, so it releases its ‘grip’.

This release allows the RNA polymerase to continue with transcription. This, eventually, turns to translation. In this stage, enzymes are created, two of which are ß-galactoside permease and ß-galactosidase (there is a third which can be ignored here). The former of the two is membrane-bound. This means it becomes embedded in the cell membrane. This quickens the transport of lactose from outside to inside the cell. Think of it like a tunnel through which only specific shapes can fit.

Once these specific shapes (lactose molecules) pass into the cell, ß-galactosidase breaks them into their constituents, one of which is glucose. This is used as a key source of energy in many organisms, including E. coli.

Once concentration falls, lactose molecules are no longer bound to the repressor, making it free to resume its normal duties attached to DNA.

RNAi: Watching Your Back

The following has appeared on For the Sake of Science. The article in the physical copy of Without Apology has slightly different wording for the sake of print.

By Michael Hawkins

RNAi is an arrestingly interesting little mechanism for protecting the health of cells. The “i” stands for interference, and with good reason. RNAi is made up of a series of molecules which work to detect and destroy possible viruses and RNA which could be viruses.

It was first detected in 1986 when an attempt was made to make a really, really purple flower. The reason was purely for aesthetics, but it would prove to be far more important.

Knowing the gene which coded for purple pigmentation in petunias, geneticists made the logical conclusion and figured adding a bunch of those genes to the flowers would increase the depth of purple coloring in them. But as it turned out, they were wrong. In fact, they were remarkably wrong. Instead of deep purple flowers, they produced white flowers. Not a hint of purple anywhere.

No one had an answer to why would be. It took 12 years until researchers came up with the answer (and another 8 until they were awarded a Nobel Prize).

When viruses invade a cell, they ‘seek’ to make copies of themselves by utilizing the available DNA source. Post-transcription, this comes out with a funny shape due to the RNA making a mirror image of itself. The RNAi then recognizes this strange shape and destroys it with dicers. But it doesn’t stop there. Any sequence which comes out of the nucleus thereafter is also destroyed. This prevents any of the viruses (hopefully) from being translated and replicating (thus exploding out of the cell and infecting other cells).

Something similar happened when the geneticists tried making the super purple flowers. There wasn’t a mirror-image RNA sequence, but there was a funny sort of shape created by all the extra purple pigmentation genes. The RNAi recognized this as a potential virus and began destroying it. All of it. This meant there were no genes for purple getting translated into proteins.

Example petunia plants in which genes for pigmentation are silenced by RNAi. (http://en.wikipedia.org/wiki/Rnai)

Example petunia plants in which genes for pigmentation are silenced by RNAi. (http://en.wikipedia.org/wiki/Rnai)

So far this is pretty exciting stuff. It’s a post-transcriptional defense mechanism against viruses no one ever knew existed. But it has so much more potential than just as a passing curiosity.

Think about it. If RNAi can essentially turn off genes by destroying them through a sort of sequence-detection, then what stops it from curing diseases? This discovery has the serious potential to cure all the major ailments facing the world today: AIDS, cancer, Alzheimer’s. There has already been success in treating macular degeneration. This is a disease where too many blood vessels are growing in the eye. It damages the retina over time and makes vision majorly cloudy and blurry. There are simply too many genes for blood vessels being produced. But one way to stop this disease is to stop that blood vessel growth. To achieve this, a patient is given an injection which contains a copy of the gene with its mirror image (two mirror strands of DNA). The RNAi detects this misshape and destroys it. It then destroys all other likewise sequences. The same principle could be applied to any number of diseases.

There is an excellent NOVA video on RNAi which can be viewed here. It’s certainly worth watching (and only 15 minutes long).

Catching Conservapedia in a lie again

From their lying front page:

Another new paper was just published in Journal of Climate. Added proof Al Gore & Company are simply lying hucksters, out for a buck. Written by eminent climatologists, called Greenland Ice Sheet Surface Air Temperature Variability: 1840–2007 which discusses data from Greenland since 1840. No unprecedented recent warming is found. For example, they find that the 1919-1932 warming was 1.33 times greater than the 1994-2007 “warming”. [19] The new report mirrors one from the United States Senate back in 2007. [20]

Just like the last time, they make the mistake of linking to the abstract they reference.

Thus, it is expected that the ice sheet melt rates and mass deficit will continue to grow in the early twenty-first century as Greenland’s climate catches up with the Northern Hemisphere warming trend and the Arctic climate warms according to global climate model predictions.

These people are kooks.