What is life?

Or here’s another description of life that has nothing to do with science. It’s mostly applicable if you’re middle class in a developed country.

To Contrast with my post: That’s life

Gattaca: Non Fiction Technology, Fictional Future

       Most well known science fiction films or television shows are heavy on the fiction but, especially when they depict any type of biology, are light on the science. Gattaca, a 1997 commentary on potential eugenics issues in the future that was written by Andrew Niccol, described a reproductive technology that is science fact now, and was science fact then. To this date, general public media attention in the United States outside of popular science magazines regarding the technology has been minimal. The technology, known as preimplantation genetic diagnosis (PGD), allows a couple to select an embryo fertilized in-vitro (in a petri dish) after genetic screening. The screening most often focuses on only a few potential problem gene variations or mutations, but could  include the entire genome or at least every part of the genome that is likely to vary without lethal results.

            PGD is one of the many new developing technologies that likely has an equal potential for humanity’s benefit and abuse. Thus far PGD, in order of least to most controversial, has been used to select against early onset terminal genetic diseases, late onset terminal genetic diseases, late onset potentially terminal genetically linked diseases, genetically linked disabilities, and gender. Many of the current applications are, at least on the surface, benevolent or even medical blessings, but, as demonstrated by texting and driving, or the proliferation of nuclear weaponry, humanity is notorious for using technology with little regard for its consequences. Because of this foible of humanity, it is only prudent that someone asks if all the current applications, even the least controversial, are truly wise.

            Selecting against early onset terminal diseases is seemingly, and truthfully, an application of PGD that has little ethical ambiguity and the only difficulty would be deciding how quickly does death have to take its victim before we a call a disease early onset and how much suffering is too much. Because of PGD, couples that would normally have difficulty bringing an embryo to term now have an opportunity to discard embryos that are doomed to spontaneous abortion. The only vaguely rational argument against such a procedure would be to suggest that the world is overpopulated and the last thing we need is another healthy baby. Alas, picking on poor couples who have difficulties conceiving a healthy embryo will not solve the problem of world population growth. Some embryos a couple can select against might come to term but are likely to die within a year afterward. Again, selecting against these embryos is not ethically ambiguous with the exception being for those who lay on the most extreme end of the abortion debate. There are terminal diseases that kill later that are selected against as well. Diseases like tay sachs, usually kill by the age of four. Most people, one would suspect, would have no moral conflict in selecting against these embryos, but likely not everyone. When PGD is used for this purpose we are faced with the task of deciding how long does one have to live  before they can have a meaningful life, as well as how much intense chronic suffering can a person endure before life becomes unbearable. After the onset of infantile tay sachs, which usually begins after six months, a child faces rapidly deteriorating mental and physical abilities becoming, blind, deaf, and paralyzed, before dying. This is probably not a child that parents, quite honestly, want to have; it would be devastating for the parents to endure emotionally, and an existence of only suffering for the child. Still, there are more possibilities to ponder. Because there are endless ways for genes to vary, there is an endless number of potential genetic diseases. Conceivably, there will be genetic diseases that kill very early but cause little suffering. The choice to select against an embryo like this may be more difficult. Is it meaningful to live for only four years? What has your four year old taught you today? The tay sachs disease has a few different variants. One variant, juvenile tay sachs may not kill until the age of fifteen. What happens when we apply the same questions to this variety of tay sachs? Finally, the third variety of tay sachs, which does not develop until adulthood, prompts a reflection on the more controversial aspects of PGD, selecting against late onset genetic diseases.

            Fertility clinics can now go beyond screens for diseases that are fatal by adolescence or earlier and identify diseases that aren’t likely to kill before, or much before, the age of thirty. From this moment forward, the potential ethical ambiguity no longer needs to be highlighted and is axiomatic. When requesting PGD a couple can now screen for huntington’s disease, and muscular dystrophy among other diseases that kill in adulthood.

            PGD has also expanded to include screens for the increased likelihood of potentially fatal cancers, as well as disabilities like down syndrome, deafness, blindness and dwarfism. Sometimes these traits are even intentionally selected . Finally PGD can be, but has not yet been, used to select cosmetic traits such as eye color, hair color, and skin pigmentation and in the future it will have even more expansive potential consequences.

            When describing this technology those who are continuing to develop it are often reluctant to concede that these diagnoses could be used to select for other traits that go beyond cosmetics and will insist that, because they are such complex traits that are equally dependent on genetics and the environment, it is too early to need worry about selection for behavior, intellect, athletic ability, or even height, but let’s be realistic; this is the 21st century. These traits are indeed very complex and even traits that are more solidly genetically linked are dependent on probability, but the rate of technological advancement continues to increase and there are ways, even now, to begin selecting embryos that may have an advantage for several reasons. At our current level of technology we have identified many genes and their variations, computer technology allows us to archive the data and make quick statistical predictions of phenotypic impact, and although many traits are highly complex, the fact is not a barrier against choice only the certainty of the impact of the choice. The certainty of a gene’s impact on any measurable human trait will be dependent upon the number environmental influences that affect it and the magnitude of their influence.What follows is a description of how many of these choices could be made now and in the very near future.

            Choices on height could already be made based on a pair of known gene variations. Height is a polygenic trait meaning it is coded for by many genes which together will have a summative impact. Unlike intelligence, behavior, or athletic ability, height likely only has a few significantly important environmental influences the most obvious being nutrition and exercise. In PGD the environmental factors must be acknowledged, but that does not mean the genes can be ignored and since it is the least environmentally dependent of the traits mentioned, and the simplest to measure, it is the most easily screened. Variations of two genes,  HMGA2 and GDF5, statistically impact height by over a tenth of one inch. These genes could be detected in PGD and thus an embryo with or without them could be chosen or rejected.

            The difficulties of screening for the other traits lies not just in their complexity and dependence on a wide array of environmental influences but also the inability to quantify such broad characteristics. Any measure of these is inherently flawed, and thus so is any one single gene association. The component pieces are however quantifiable and they are therefore subject to PGD.

            Athletic ability can depend on an array of traits such as muscle fiber type, ventilatory efficiency, i.e. how well the lungs function, cellular respiration or how well an individual’s cells use oxygen to burn fuel, and the ability of the brain to coordinate movement and balance, among countless other components. Also, there are many kinds of athletes. The best lungs for swimming may not be the best lungs for running, weight lifting, or basketball. So selecting for athletic ability overall is highly problematic but you might select traits that predispose individuals towards greater success in specific physical activities. At this point, research suggests that the distribution of muscle fiber type in a individual is highly to completely independent of genetics but there are still plenty of other types of traits that could be examined in PGD that would affect athletic ability. Muscle mass is one obvious potential by examining variations in the MSTN myostatin gene, a gene that has seen significant agricultural and medical attention because of its action as an inhibitor of muscle growth. This gene need not be screened directly, but rather one might examine the genes that regulate its expression and thus select an embryo that likely has it turned on or off more frequently. Another aspect of athletic ability is dependent upon the level of control an individual has over their own body and reflexes. All the control comes from the nervous system, the source of behavior and intellect.

            An intelligence quotient is far too broad a measurement to link to single genes and behavior is a consequence of intellect and physiological reflexes, but again, if these complex characteristics are broken down, specific traits for intellect and behavior can be found and selected for or against in PGD.

            There are several readily quantifiable measures that are  components of  intellect. Memory is the first most obvious aspect and it can be broken down into smaller categories like short term and long term. These too can again be broken down into the even more specific categories, implicit, and explicit. The anatomy, cellular, and molecular biology of the action of memory has already been described in some detail, and while it is no means comprehensive, it does provide an excellent starting point for finding genes related to intellect. Despite the growing understanding of memory at the molecular level, there are still no known genes that are linked to even a minor memory enhancement or impairment. Still, its just a matter of time, and likely not a very long time.

            When an individual is confronted with foreknowledge of their potential offspring, choices could become difficult. It would not be easy to choose an embryo that will most likely die before they reach the age of six. Can someone have a meaningful life in such a brief time? I might ask you what has a four year old done to change the world. The answer can actually be quite surprising. At the age of four, Alexandra Scott of Connecticut began a lemonade stand to raise awareness of cancer varieties the affect children as she was diagnosed with neuroblastoma. She raised 2000$ with her first stand and it led to the creation of a foundation that has raised 60 million for cancer research. Many will remember her as she did get a fair amount of media coverage. Alex’s story is by no means typical but the mere fact of its occurrence makes embryonic selection more ambiguous. On the other hand, there need not be awareness of neuroblastoma if it were entirely genetic in nature and everyone had PGD screening for it. Regardless, Alex’s example demonstrates that even a brief existence need not be an empty existence and those who live into their teenage years have a greater chance of making a large contribution to the world.

            Diseases that kill in adulthood threaten to kill early enough for many parents to outlive their children, an undesirable event. Thus, faced with the choice between embryos that will have a fatal disease or have a relatively high probability of contracting a fatal disease in early adulthood and one that has little likelihood, most prospective parents will select the embryo that is healthiest. The ones with potential diseases will not be born. The argument over these applications of PGD can be distilled down to this; is it ethical to intentionally deny an embryo birth based on foreknowledge of its potential fitness? The key word in the preceding question is “intentionally”. Likely all opponents of abortion will find every application of this technology that goes beyond helping a struggling couple bring a child to term quite horrific. For those who are pro choice, there are other aspects to consider. The embryos in PGD don’t get more than 8 cells big before being screened. While they will never be born, most potential genetic combinations aren’t. The number of people who are born every day is infinitesimal compared the number of potential people that aren’t born. The only difference is that fertilization occurs before being denied birth and PGD begins to remove the randomness of the selection.

            In evolution, individuals that are less fit for survival are less likely to successfully reproduce before dyeing and their less fit genes are less likely to be passed on, but what’s fit now may not be the most fit one hundred years from now; fitness changes based on environment. How then, do we determine the difference between a disability and a simple variation? Being born blind or deaf during the infancy of Homo sapien history probably would have been fatal, but now it does not prevent anyone from living a perfectly happy, healthy life as we have altered our environment to separate a potentially unfit trait from an individual’s ability to survive and reproduce.

            For some, fitness may not be enough, and PGD has the potential to select for greatest fitness in what would be, at best, minor ways now, but will likely continue to be more impressive in time. Unless the application is universally available at a price everyone can afford, this application will likely incite violence. Even if it is free to the world it is unlikely that the use of PGD in this manner will not cause dangerous conflict.

            An extreme lollipop and sunshine optimist might imagine a scenario where the benefits of this technology are free and equally available to anyone in the world from the loftiest filthy rich executive to the most feeble meth head writhing about like a worm in the dirt of poverty. In this scenario, the strife between the rich and poor can be ignored if everyone, regardless of social class and station in life, has the option to select the best from a sample of their own embryos. Still, despite universal availability, some will choose not to participate. That will be their own choice. However, regardless of the reasons those individuals have for not participating in this reproduction enhancement, they may not feel comfortable with those around them that are selecting their children to have a genetic leg up. Those that reject the use of the technology based on religious objections will be harboring moral outrage that goes beyond that directed towards an abortion. Abortion is often perceived by some as the murder of babies, but PGD takes it one step further and might be perceived as an interference with god’s plan or natural order. Because the children of those that do not reject the technology may be gaining a genetic advantage over the children of those who do, they might even view it as an attack on their religion or, worse yet, their children. Those that reject the technology through morals unguided by religion will also likely experience unease as one group of people grabs a reproductive advantage over them. Chances are that, just like the current situation with violence against abortion clinics, a few fanatics will take action in such a best case scenario.

            The preceding hypothetical was quite rosy but is probably about as likely as world peace. Humans, by their very nature are selfish and exclusionistic especially when it comes to their children. The use of PGD beyond the very basics will most likely be limited to the wealthy. Only those blind to reality would believe that when this occurs the other less monetarily privileged will feel just fine about the wealthy stacking the deck biologically as well as financially. Monetary inequity extends beyond internal strife within the United States. It is the greatest source of friction between foreign entities, and if it grows into perceived biological inequity, the justification for war will extend beyond resources and religion. We can’t afford to delay informed public discussion about this technology.

 Before this technology becomes fully entrenched in our culture it might be a good idea to very carefully consider each of these questions.

1. How do we evaluate and define a disease state?

Why this question: Some genetic diseases, like sickle cell, are distinctly maladaptive, but others are more ambiguous. Dyslexia for example doesn’t necessarily enhance or inhibit personal achievement. Also some diseases are defined very poorly. For example ADHD is controversial and lacks solid definition.

2. Where do we draw the line between disease and variation or preference?

Why this question: Some inherited traits may be only slightly detrimental if at all. Are albinism, dwarfism, or deafness diseases states or variations. If nobody chooses to have children with these traits, do we lose out on valuable diversity?

 3. How can we ethically embrace this technology if an entire segment of the world’s population opts out either voluntarily or by financial force?

 What do you think? Discuss

Contrary to the tagline of Gattaca, there are genes for human spirit. A more accurate lesson would be as follows: Even the most improbable events are still possible.

Atoms are mind boggling: Want not for of not is what you are made.

Atoms are the smallest unit of matter before matter starts getting weird.

Atoms typically behave in predictable ways to maintain stability, and on the surface, they fit intuitive and logical notions that do not challenge human understanding about the nature of reality, but when scientists began to peel back the surface, they found Alice’s rabbit hole. Inside the atom lies, a teeny tiny nucleus of protons and neutrons, an electron, and, between them, a vast expanse of empty space. Everything that is, mostly isn’t. All things are mostly nothing. Crazy, isn’t it? Unbelievable!

 How empty is it, and if atoms are empty, why does matter seem solid?

Atoms are small, smaller than humans can realistically imagine (unless you can imagine something a 10 billion times smaller than a meter, i.e. 100 picometers), so it useful to imagine them as larger to understand how empty they are. In a typical atom, the radius of the nucleus is 20,000 times smaller than the radius of the atom. In some atoms, it can be 100,000 times smaller. That means if the atom were as large as the earth with a radius of approximately 6400 kilometers (4000 miles) and the nucluer radius is 20,000 times smaller, the radius of the nucleus would be less than 1/3 kilometer (1/5 mile). All the rest of the earth would just be space for the electron, which is odd given that, near as anyone can tell, electrons have no volume.

How can anyone reconcile this empty notion given matter’s apparent solidness? It’s easier when one considers the fact that electrons are extremely fast. They are almost impossibly fast at a speed approaching 300,000 kilometers/sec (186,000 miles/sec). If they were one iota faster, they would literally be impossibly fast. At that speed, an electron can travel the circumference of the earth seven times in one second. Imagine how many times it can travel around a space that’s submicroscopic (note: electrons do not orbit a nucleus like a planet orbits the sun). Electrons are virtually everywhere at once within their atoms radius. The fact that electrons are everywhere at once makes matter solid. At least sort of; its actually more complicated than that. There are other factoids about subatomic particles like electron repulsion and the pauli exclusion principle that also make atoms more than mostly empty space.

Stay tuned for definitions of electron orbitals, energy shells and their relation to biology.

-Loup Mal

Matters of the Heart

Once a girl I was infatuated with explained to me that we could never be. She told me I could not know what was in her heart, you see. To which I replied, Au contraire, my lady fair. I know a great deal about what’s in your heart. I said that, with me, she would feel complete, for I could tell her what made her heart beat.

No matter what you may try, you can not empty your heart out.

Relentless, indefatigable, metronomic, the heart never ceases its rhythm only alters it. Each beat is like a grain of sand plummeting through the slick and slender gooseneck of your life’s only hourglass.

Why does the heart beat?

Early in development the heart attracted company

A couple of guests from the neural crest

They were an envoy of cells never at rest

Relentless and cogent or so I am told

The invaders engendered the sinoatrial node

From there they spread their corruptive excitation

They spread their missive of  salacious contraction

It spread to the cardiac myocytes of the atrial abode

The missive had consequence; t’wasn’t just symbolic

It triggered an event that was unarguably atriosystolic

And there was another nodable ally for the polarizing politic

Its existence foiled barriers fibrous in particular

It was a node simply named as the atrioventricular

The message did not dwindle or grow very stingy

It traveled through the branches and fibers purkinje

They extended the function of conduction vehicular

Fear not the unrest could not last; fleeting it has to be

There was to be peace, a moment’s respite; they call it diastole

Still, the sinoatrial stirs and the struggle continues unendingly

Needless to say, she did not understand.

The Categories of Life: Why “Animal” is not a Dirty Word

Being dirty can be fun, but it has nothing to do with the definition of an animal.

Biologists study living things known as organisms. Organism is just a generic term that means a living thing. There are countless kinds of living things, and, for scientists, the most natural first step to understanding living things  was to divide them into categories. I have already posted on this briefly in my fungus article, and the first  paragraph of what follows is pasted directly from that post with minor modifications. The rest continues with a more complete description of how the categories are defined and distinguished from one another.

Some of the categories are extremely broad, and some are extremely specific. As an example, imagine automobiles. Automobile is a very broad category that can include anything with an engine and wheels that carries passengers along roadways, but as everyone knows, automobiles can be organized into more specific categories like trucks, vans, cars, motorcycles, and buses. Those categories can be broken down into even more specific categories. The category of cars, for instance, can be split into yet even more specific categories like station wagons and sedans. Biologists organize life into categories the same way, and they have terms that describe how specific the category is. These terms are called taxonomic levels. The taxonomic levels in order from broadest to the most specific are as follows below:

Domain

Kingdom

Phylum

Class

Order

Family

Genus

Species

The broadest categories of life are organized into domains. A domain is a relatively new taxonomic level that was proposed in 1990 by a group of microbiologists. There are three domains, eubacteria (you back teary uh), archaebacteria (are key back teary uh), and eukaryota (you carry oh ta). The three domains are split up based on the structure of their cells. For instance, in all three domains the cells have membranes and DNA, but only eukaryotic cells have a nucleus (new clee us). That’s why they are in a separate domain category. The other two domains only include kinds of bacteria. Eukaryota, includes all other known living things and is split into more specific categories that a non-biologist might find more familiar.

The next taxonomic level of categories is called kingdom. The eukaryotic domain consists of at least four kingdoms, animalia (ani mail E uh), plantae (plant eh), fungi, protoctista (pro tock tist uh). Because they are in the domain eukaryota, every living thing in these kingdoms, by definition, has a cell or cells with a nucleus. As one might guess, kingdom animalia is a category that contains all the animals, kingdom plantae all the plants, and kingdom fungi, all the fungi. The fourth kingdom, protoctista, is more complicated. It contains all the single celled or extremely simple multi-celled organisms that don’t quite fit into any of the other three kingdoms in the domain eukaryota. Currently, biologists are working to clean this messy kingdom and split it into more accurate and descriptive categories. The other three kingdoms, while not perfect or unchanging, are more distinct and well described.

Kingdom plantae contains all the multi-cellular eukaryotes that have a cell wall made of cellulose, chloroplasts, and transform energy from sunlight into sugar. Kingdom fungi contains all the multi-cellular eukaryotes that have cell walls made of chitin that release digestive chemicals and then absorb the broken down nutrients. Kingdom animalia contains all multicellular eukaryotes that have no cell wall and take in nutrients by ingestion. Biologists have broken down each of these kingdoms into more specific categories but listing and describing them all is a task for a giant book and not a blog post. For example, the next rank in the animal kingdom, phylum, has thirty-five categories. Instead, it is more useful to describe one animal and how it fits into one category along each taxonomic level. Below is an example of the categories that humans fit into along each of these taxonomic levels. Included as well are distinguishing characteristics, things that set one category apart from another category in the same taxonomic level.

Humans

Domain: eukaryota – Humans fit into the domain known as eukaryota. All eukaryotes, including humans, by definition, are living things that have a cell or cells with a nucleus.

Kingdom: animalia – By definition, all living things in the domain eukaryota are multi-cellular organisms that lack cell walls and ingest nutrients are animals. Because humans are multi-cellular eukaryotes that ingest nutrients and are composed of cells lacking cell walls, they are placed in this kingdom category.

Phylum (file um): chordata (core da ta) – All animal eukaryotes that have a notochord (no toe cord) are placed in the chordata phylum category. A notochord is the origin of the backbone and humans have one. Therefore humans are chordates.

Class: mammalia (ma mail E uh) – All chordate animals with fur/hair and mammary glands (milk producing glands) are mammals. Humans have mammary glands, and no amount of waxing or laser surgery will change the fact that humans have hair follicles. If humans were not mammals, their would be no point in joining the hair club.

Order: primates – Primates are all mammalian chordate animals with binocular vision that can rotate their shoulder joints. That ball and socket joint in the shoulder allows us humans to rotate our arms in all sorts of useful ways, and binocular vision from eye placement in the front of the head, instead of on either side, provides depth perception. If humans weren’t primates, 3-D movies would be silly. Note: the characteristics mentioned above do not perfectly describe the primate order and it is continually revised and refined.

Family: hominidae – All primate mammalian chordate animals with bone and muscle structure modified for bipedalism (walking on two legs) are hominids. Moving about on hands and knees doesn’t alter bone and muscle structure; humans are hominids. The hominid family is constantly refined and revised. Some biologists and anthropologists think that gorillas, chimps, and orangutans should be part of this group and others do not.

Genus (jean us): Homo – Humans are in the genus Homo. All the other members of this category are extinct. Humans as well as all the extinct members of this genus walk on two legs exclusively. This is different from hominids like gorillas or chimps that can walk on two legs but don’t move great distances. The defining characteristics of this genus are still being refined and revised.

Species: Homo sapien – Only humans are Homo sapiens and all Homo sapiens are eukaryotes, animals, chordates, mammals, primates, and hominids. Homo is the genus name and sapien is the species name.

Notice that the species was presented in italics and was preceded by the genus. Also the genus was capitalized and species was not. It’s slightly incorrect to forget to italicize the genus and species name or forget to capitalize, but it’s extremely incorrect to name a species without putting the genus name in front. Doing so can lead to confusion.

Knowledge of taxonomic levels and the categories of living things is typically presented  within the first or second month of a high school biology class, but many people I encounter have the misconception that only vertebrates or mammals are animals. They either never learned, or forgot that things like insects, clams, and tape worms are also animals. To reduce confusion, a few examples of other categories at each taxonomic level are provided below. All the eukaryotic kingdoms were listed, so the examples start at the phylum level, end at genus, and are all from the animal kingdom. Common name examples are in parentheses.

Phylum: arthropoda (insects, lobsters, shrimp), cnidaria (jelly fish, corals), annelida (worms with segments)

Class: insecta, cephalopoda (octopus and squid), reptilia, oligochaeta (earthworms)

Order: carnivora (carnivorous mammals), hymenoptera (ants, bees, wasps), decapoda, unionioda

Family: mustelidae (weasels, badgers, otters), formicidae (ants), architeuthidae (a specific group of squid)

Genus: Canis (wolves, dogs, dingoes), Pheidole (weaver ants), Alatina (type of box jellyfish)

Again, all of the above living things, like humans, are kinds of animals. Unfortunately, some people get offended when reminded of this fact. Animal is not a dirty word and there is no reason to be offended. The discomfort is also inconsistent. People rarely take offense when you remind them that they are mammals, a group included in the animal kingdom. What is the origin of their outrage? It seems to be the association between animals and the base desire to compete, procreate, and take in nutrients without restraint. Well, good news everyone! None of these sinful things have anything to do with the definition of an animal in biology.

There is nothing in the taxonomical description of the animal kingdom that states that these drives are a distinguishing characteristic of animals. As previously stated, being multi-cellular, having cells with nuclei that lack cell walls, and the need to ingest nutrients, are the only characteristics necessary for animal status. Any argument against animal status must demonstrate a fundamental difference between cell structure and physiology. For those who take offense from a reminder of animal status, it’s worth asking what’s offensive about being an animal. Is it having eukaryotic cells, being multi-cellular, or taking in nutrients? Likely no one will consider these things offensive.

Those characteristics that some find offensive are not exclusive to animals, but rather are characteristics of life. Is being alive offensive? It would be impossible to argue that humans are not alive, but if anyone wishes to have an intelligent argument about the taxonomic description of humans and the relevance of restraint against base desires, there is a place for these discussions in biology.

Humans are animals, but not just animals. Our distinctions from other animals lie in the complexity of the part of the brain known as the cerebral cortex as well as perpetual bipedal locomotion. Constant bipedal locomotion is the most easily measured difference between humans and other mammals, but the complexity of the cerebral cortex and the consequent accomplishments are our greatest source of pride. Any discussion about what makes humans special will center on these things. For example, some biologists argue that the rudiments of language are a part of the distinguishing characteristics of the family hominidae. Understanding how we are special depends on neuroscience studies and studies that compare and contrast humans to other hominids. Whatever the findings of these studies, none of them will change our status as animals. It’s OK. Remember, animal is not a dirty word.