Mendelian Inheritance

Many people think genetics works like this.

While it is certainly a wonderful joke, this isn’t exactly what happens. Indeed, Dawkins devotes a few pages on this in The Greatest Show on Earth. Mendel actually discovered something contrary to the “blending of traits.” As Dawkins states, if traits were indeed a mix of the traits of each parent, we would see children with a combination of the traits of both parents, grandchildren would receive traits from all four grandparents, and, very quickly, diversity would decrease to a homogeneous blend. Dawkins uses the “mixing paint” metaphor. If you mix red paint and blue paint to get purple paint, no quantity of mixing will ever yield the original red or blue paint again.

So what, exactly, are the Mendelian laws?

The Law of Segregation states that when gametes are formed, the specific traits previously inherited from the parents are separate entities and are segregated from one another with only one of the two being inherited by offspring from each parent.

The Law of Independent Assortment states that traits from the same parent are not linked to one another. This means that the offspring can inherit a trait from one parent and a different trait from the other parent. While many genes are technically not “dominant” or “recessive,” traits can be. Most often, genes are coexpressed in differing cell populations or, sometimes, in the same cell. The traits resulting from one specific allele can appear to mask the traits of the other allele.

This is a point which needs further clarification in the very near future.

Oh, the inanity

Here’s something that should be a bit of a non-starter of an issue.

The work is expected to take at least a year, but its leaders hope it will help establish guidelines for scientists in Britain and around the world on how far the public is prepared to see them go in mixing human genes into animals to discover ways to fight human diseases.

Genes cloned from humans with diseases to develop model organisms to study diseases. I’m not sure exactly why anyone would have a problem with replacing the gene for a protein found in a specific organism with one from a disease-type gene found in affected humans.

“Do most of us care if we make a mouse whose blood cells or liver are human? Probably not,” he said. “But if it can speak? If it can think? Or if it is conscious in a human way? Then we’re in a completely different ballpark.”

I still fail to see how this is an issue. First of all, every vertebrate has some level of thought processes (read: they think) and thus we are trying to draw an arbitrary line in the sand. Secondly, can we cross that bridge IF we get there (which I highly doubt we would, when working with mice, rabbits, and yeast). Thirdly, why is vocalization and communication so important to this notion of “conscious?” Let’s have a real debate, and it should start out with questions such as “what are the reservations of the public against the use of human genes in model organisms?”

If the reply has anything to do with “it will make them like us, and we can’t experiment on them because they have our DNA” then educated individuals in the audience should appropriately laugh these individuals off the stage.

DNA does not a human make. We are more than our DNA, we are a combination of embryological conditions, biochemical and physiological stimuli, and developmental conditions interacting with other molecules to produce a human. Quit thinking of an organism in simple terms, DNA isn’t the organism, it is a part of the organism, providing the reactive templates for synthesis of other molecules and interacting with many highly variable signals in complex ways. While certain changes in the DNA can results in specific physiological changes in the organism, it is a result of the interactions that such a physiological condition arises. If the interactions change (read: restorative mutation) then the condition may be present with the original molecule rather than the “disease-state” molecule. Biology isn’t simple, making public policy decisions about scientific research should not be done while assuming a blatantly false, overly simplistic model. I’m all for informed debate, but this is why I do not debate many people. If someone asks questions, I will gladly point them in the right direction, if someone has an incorrect idea of biology and makes reasoning errors as a result, I will help. If someone wishes to argue and refuses to listen to my side because they are utterly convinced of this simplistic model, it is a waste of time.

The Physics of Homeopathy

Ever wonder how homeopathy is supposed to work? Well, Charlene Werner wants to explain to people how it works!

Here’s the video, but I’m going to be kind enough to transcribe it, so you have the option of just reading it rather than giving it another page hit.

Well, thank you so much, I’m going to explain to you exactly, actually how it works. Now, has everybody had chemistry, like, uhm, in school, way back when? But you do know what H₂O is, ok. And have all of you heard of Einstein? Ok, you know that light is energy, right? And he gave us the theory that energy equals mass time the speed of light; e=mc². Ok, now if you take that formula, and we think there’s a lot of mass, right? Ok, if you collapsed all the mass down into the universe so there is no space between the mass, do you know how much mass there is in the entire universe? You think you’re a lot of mass, right? I’m a lot of mass, this building is…[laughing] Well, the whole universal mass can be consolidated down into the size of a bowling ball, that’s all there is in the whole world, in the universe. So how much mass are you? That’s right, an infinitesimal amount. So if you take that formula, e=mc², you can almost cross out mass. So the formula ends up being energy equals the speed of light. Ok, and that’s why the vision system is so important. Because we have lots of photoreceptors that receive light. But when Hahnemann died, he, uhm, the scientists didn’t fall in his camp. Ok, and uhm, the pieces of the puzzle didn’t fit well together. So god in his infinite wisdom send him another Einstein called Steven Hawkings [sic: see Stephen Hawking]. Ok, Steven Hawkings [sic] gave us the string theory, and what he discovered is that there are other energetic particles in the universe and they are shaped like little “u-ies” and what they do is they work by vibration so our body is so wonderfully designed; we have light receivers, and we have ears, string, vibratory, they pick up vibration, so if you add it to that theory, Einstein’s theory of relativity, we have e=mc², that mass is crossed out almost, and strings, vibration. But that still doesn’t tell us the whole picture. Because what is a cell? Right? So a cell has cell walls, cell membranes, cytoplasm. Is that mass? Not very much, really, so what are they, what is that? You can break down the cells into tiny pieces of energy, called electrons, protons, neutrons. So the whole body has an infinitesimal amount of mass, but what is the remainder? Energy. So I am energy, you are energy. Now if you go to study physics, energy cannot be created, we do not know how to create energy, but we don’t know how to destroy it either. That is not humanly possible. So what we do is we take energy and we transform it from one state to another. That’s all we do, so if that’s all we do, guess what the definition of disease is. It’s not mass, we have transformed our energy state into something different. That’s what the definition of disease is. Ok, so we should be able to retransform our energy into a previous better state, right? So what we do is we use light, we use sound, we can use homeopathy. Ok, so what is homeopathy, if nothing is really mass, or an infinitesimal amount of it, and everything is energy, that means everything has a vibration to it. Ok, so what if I could encase some sort of energy for later use? Ok, so, if I wanted to make a bomb, and I took all these chemicals and encased it a..a bomb, and tonight, my neighbor lets his dog poop in my yard, literally, and I’m mad at that dog, and my neighbor, so I’m gonna take this bomb, and I’m going to get back at him. So what if I threw that bomb at his house, would he be happy with me? Because what happens now when that energy is released? It destroys something, or changes it. It makes the building now not in structure form, it changes its energetic state. Well that’s what we can do with homeopathy. We take substances and what we do is we, we pulverize them, and we put them in solution, and we succuss it just like the bomb, we threw the bomb, to release its energy into this liquid, and then we take these little white pellets, we sprinkle them with that solution, and guess what we have just made? An energetic substance to be used when we choose to use it. Ok, so how homeopathy works is, whatever your disease process is, it’s an energetic change, and if I can find the remedy which matches your state, and give it to you when we so choose, what can we do with your energy system? Transform it to a previous better state. And that’s how it works.

She then goes on to even more nonsensical stories….

Now, I’m sure you, like myself, are completely dumbfounded by how much nonsense is in this talk. I might subject this to a thorough fisking… Oh, what the hell, let’s go

Simplifying vs. Oversimplifying

Or

My conclusions on falsehoods

I’ve explored quite a few falsehoods to some depth recently, and I have a few very general thoughts on this matter which I would like to share.

So much of our understanding of reality is reliant upon language which does not allow for simple explanations of what is actually occurring around us. Our brains operate at the “vertebrate organism” level. We have no innate mechanisms to think in terms of geologic time, subatomic movement, or galactic dimensions. We also have no intrinsic ability to grasp long-term population genetics or ecological changes. Instead, we must use metaphors which are often mistaken to be the truth in themselves.

Humans also have a tendency to find causality and patterns when none exist. We notice images in completely random static, faces from completely different shapes, and order in piles of debris. This pattern-seeking behavior is particularly problematic when dealing with causes lacking agency.

Additionally, humans love nothing more than simple explanations. This is where the falsehoods come from. Simple explanations which make the complex issues we notice seem to make sense upon casual observation. These falsehoods in themselves are not a problem so long as the individual knows these are only metaphors and representations. Expecting a ten second summary to explain all of the research on a given topic over a period of years, decades, centuries, or (in some cases) millennia, is a requesting too much from the language. Our communicative technologies and techniques are not sufficiently developed to allow rapid transmission of this much information.

This is where the difference lies between indoctrination (classical definition) and education. Education is to lead to a conclusion, while indoctrination is to present only the conclusions with no reason for belief, the conclusions in this case being the condensation of experiential data, models, and ideologies all rolled into one. I firmly believe, for example, that it is possible to explore an idea with someone and lead them to the same conclusion as would be produced by simply presenting the preformed conclusion. The only distinction is that, if new evidence comes to light, the conclusion which one has been led to can be adapted piecewise to include the new evidence whereas without the evidence supporting the previous conclusion, it must be dismissed wholesale.

Falsehoods: Mutations are completely random

This is a fun one. We’re always told that mutations occur randomly throughout the genome, but this idea kind of misses the point that they are, in their own way, “predictably random.” At different parts of the genome, mutations occur at different frequencies. On the individual level, different types of mutational causes are more frequent than others. Each site along the DNA has a mutational variance based upon conditions the region is subject to. This is why the various “molecular clocks” need to be calibrated separately from one another. We have many molecular clocks, indeed, we are limited only by the number of common genes between organisms. Indeed, the LUCA (Last Universal Common Ancestor) possessed at least:

rRNA and tRNA genes
DNA-binding genes for topoisomerases, ligases, and repair proteins
RNA polymerases
glucose metabolism genes (hexokinases, at least)

80 genes, all told. This is useful if you’re comparing a specific bacteria to a specific bird, but many species share more genes than these. Mammals, for example, share more genes with each other than they share with yeast and plants. This is only to be expected, but I’m getting off topic. Different genes mutate at different rates, and these rates vary based upon several factors. One of which being the DNA repair and replication genes of that organism. Some repair and replication proteins are notably more efficient at repairing or replicating DNA with higher fidelity. This variance in fidelity plays a role in mutation rates. Broadly speaking, however, the introns of these genes vary little within families and orders due to the selective pressure to have functional DNA repair and replication genes. The rates are about 1/50th that of silent stretches of the genome.

Another point is that mutation rates are not exactly correlated to years, but to generations, so a shortening in generation time will lead to an increase in the mutation rate and vice versa. Yet, once again, the increase will be more pronounced in the silent stretches of DNA than in the functional stretches.

Additional compounding factors include the methylation/acetylation states of histones (at least in eukaryotes) which allow more or less exposure to the repair proteins found within the cell. For this reason, (generally speaking) genes bound by highly methylated histones tend to undergo higher mutation rates than those around demethylated (or specifically methylated) histones.

Moreover, the different molecules which comprise DNA differ in their interactions with neighboring/paired molecules. Two thymines next to one another can fuse to form dimers if exposed to UV light. Cytosine can spontaneously deaminate to form uracil. Mismatched pairs vary in frequency due to variations in partial affinity.

These are certainly not ALL of the problems with the idea of absolutely random mutations, but make for a decent start on the issue. We have to understand that while specific mutations occur randomly in terms of if or when they will happen, the rates of mutation differ due to various compounding factors.

Sorry

I’ve been rather dormant, but I have a few things I was working on which I need to finish… Wednesday night in the hospital for dehydration; 4 liters of saline, a barium sulfate contrasted CT scan, IV antibiotics and antifungals, I’m feeling much better. So I hope to resume posting again tomorrow, but for now, I’m going take a nap…

Performing Kinship

It has taken me some time to complete this review, and for that, I apologize, I do hope the wait was worth it:

Krista Van Vleet sets out to explore the lives among the natives of the Sullk’ata region. In doing so, she establishes the role of ritual, exchange, and nurture which play roles in relatedness among these people. She does so by recounting stories told to her by the inhabitants and drawing upon observations from her time with them. In exploring the culture of this region, she not only illustrates their rituals and traditions in contrast with that of western society, but also explores our own culture as well. This is the primary reason for my reading this book and that which I took away from her writings.

The interactions of parents, spouses, children, and siblings only begin to illustrate the relationships among the natives of this region. Highly complex relationships exist within the exchange community known as one’s ayllu. The ayllu is developed over one’s lifetime extending to, as we would call in western society, relatives and in-laws, and to neighbors, friends, and more distant genetic relatives. Van Vleet illustrates these exchanges and interactions with a series of stories illustrating the complexity and subtlety of these relationships. She tells the story of a child, Javier, who had “two mothers,” in the sense that, when his birth mother (Julia) was unable to care for her child, the responsibility was given to her sister (Silveria) who provided and cared for him as a young child. Javier, in the sense of children being the receivers of food and nurture, was the child of both Julia, who cared for him from birth until her injury, and Silveria, who cared for him after Julia’s injury until she had recovered.

Children, in this culture, are nurtured by the parents. Parents are, upon the child becoming independent, given gifts from their children as a sign of love and gratitude. Silveria was upset when Javier failed to bring her a radio as he had done for Julia, insisting that Javier his mother.

While the story of “Javier’s Two Mothers” is used to illustrate how children, in a sense, are the child of the parent, it serves additionally to give insights into how Julia’s sister assisted her when she was unable to care for her child. Additionally, children can be “loaned” to couples whose children have all moved away. This serves to release the burden upon the childless couples to complete all necessary work for their subsistence, but also removes some of the burden from the parents with many children. This exchange of labor (ayni) is one of the corner stones of their culture.

Van Vleet illustrates this in a wonderfully short, but information rich, ethnography containing insights into conflict and resolution, violence and abuse, sexuality and alcohol, as well as many other aspects of life in Sullk’ata. She explores both the said and unsaid, the distinct and frighteningly similar, aspects of their culture. She further explores marriage and the integration of Catholic requirements upon civil marriage and how these requirements have been integrated as another layer of reciprocity is added upon the already quite complex exchanges of the ayllu.

The only real fault I found with this book is the complexity with which it explains. For individuals with only minimal knowledge of anthropology, it makes for quite a difficult read, however, with a bit of extra time and parsing the arguments thoroughly, it is quite easy to understand. Most of her claims are, if not at least intuitive given the narrative associated with it, fairly well explained and supported by additional references.

Finally, I fear I cannot possibly give this book a thorough review due to my lack of familiarity with cultural anthropology, but I have tried even so. Anyone with an interest in viewing, not just life in Sullk’ata, but also life in our own society, through new eyes would be encouraged to read this book. It will not give you a comprehensive guide to the lives of these people, but it will give you insight into our own lives. You may even come away as I have, wondering why we do some of the things we do.

And now for something completely different

Rarely do I talk about domestication (ok, so I’ve never talked about it before). I just figured I’d share a bit of interesting things about the domestication of the date palm. The wild stock from which the date palm originates was identified by Zohary and Spiegel-Roy in 1975. The fruits of wild form of date palms are smaller with very little pulp (the tasty part around the seed) and are very bitter and indigestible with only a few wild individuals actually being palatable.  It is easily seen, however, that these palatable phenotypes were eaten and subsequently planted (either intentionally or accidentally) near human settlements. Populations were already sessile owing to the previous domestication of grains and pulses. (~11,000 yBP) That means the trees which tasted better were more frequently eaten with the pits discarded near the settlements. Domesticated date palms were being cultivated within 7,000 years of the domestication of staple crops as recorded in cuneiform tablets dating to 4000 yBP. Additionally, written records from the first Babylonian dynasty indicate that date palms were already being hand pollinated by that time.

Submission

Perfect defacement, or would it be considered improvement?

The Greatest Show on Earth

In case you have not read Dawkins’ latest book, “The Greatest Show on Earth: The Evidence for Evolution,” I highly recommend it for those of you with only a cursory knowledge of evolution or biology in general. While it is by no means a comprehensive documentation of all the evidence for evolution, it does touch on many fallacies and arguments often put forth against evolution. However, it does much more than this. It describes, in classic Dawkins style, a rather broad sample of the fossil, molecular, biogeographical, embryological, and experimental evidence for evolution ranging from Lenski’s experiments to Endler’s guppy experiments and many others. Even those that have taken college courses in evolutionary biology, but have not kept up with the literature of the past decade or so would greatly benefit from this book. While I disagree with many of Dawkins’ metaphors, such as DNA “code” and other falsehoods, I nevertheless think these falsehoods are useful in the introductory style or writing in which they are used for only a basic introduction. In fact, I may even go so far as to say these are necessary for this particular target audience. For those of you at least moderately familiar with evolutionary biology, Dawkins may not tell you anything new (or he may), but his manner of explaining this demonstrates, if nothing else, a useful model in how to present this information to the uninformed.

I must admit I am genuinely unimpressed with this book in terms of information contained within it (I knew about pretty much everything he covered except for the lack of fossil flatworms and a few other points), but I am very impressed with what I have learned reading between the lines regarding how Dawkins presents this information.