Information is Important

Information is important. With information each of us as individuals, and our society as a whole, can learn about the world. With information, we can all make decisions that make sense. With information, we can all discuss ideas.

Without information none of that is possible. Without information, we are, at best, at the mercy of our current, limited knowledge, and our base instincts. Without information we are, at worst, at the mercy of the limited knowledge and instincts of someone else.

This is why the gag order, and insistence that all reports and data be pre-screened before release to the public, issued by the President to the EPA are so concerning to me, and I think should be so concerning everyone else. This is exactly the kind of action that limits access to, and spread of, information. It will only hamper all of our abilities to operate as rational, critically thinking individuals. It is the kind of action that is put in place to control what we, as citizens, know and when we know it. This is censorship and it has no place in science or a free society.

#thisisnotnormal

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Seeing

Being able to see what is in front of you is an important skill. This may seem like one of those statements that is so obvious that there is no point making it. However, it seems to be a skill that is difficult to master. Recently, I have been running into this issue a lot. As I have mentioned in other posts, I am a Teaching Assistant for an introductory biology class at U.C. Davis on Phylogenetics and Biodiversity. A large part of this class is exploring how organisms (plants, animals, fungi, microbes, etc.) are similar to, or different from, one another. This requires students to actually look at organisms and determine these similarities and differences, and here lies the rub. Getting college students to simply describe what they see is frequently a real challenge. We will be looking at an organism and when I ask them to tell me what they see, they immediately begin telling me what kind of organism it is. That is not the same thing. I am asking them to describe what is in front of them (a soft body, two openings for water, no skeletal support system) and instead they are giving me labels (a Tunicate).

And this phenomenon is not limited to college students. I have been a birder all my life and sometimes lead birding walks for various organizations. I have often asked other birders I am with to tell me what they see when looking at a particular bird. Their tendency, young birder and old, is to start attempting to put a name on the bird. Instead of looking at the bird and letting what they actually see guide them to an identification, they jump ahead and start putting names on the bird that often basically amount to guesses. Over and over again, in so many different settings, I have seen this kind of thing happen, and it is always because the people looking at the world are not able to slow down and really see it!

This need to rush to a label is really troubling for me. I know humans have a sort of innate tendency to want to put things in boxes, but surely we should be able to overcome that tendency. We should be able to look at an object and just take it in. Make note of what you see before you and let that information guide your thinking. The desire to put a label on something reverses this process. By putting a label on an object, we are biasing what we think that object will be like.

I have seen this happen in the birding world so many times! Someone will see a bird. Great! They will not know what it is right off the bat. Nothing wrong with that! So they will ask for help in identifying it. Wonderful! Then the problems start. Instead of looking at the bird are really seeing what is there to see they jump to the identification, the label. Since they did not know what the bird was, the label they jump to is often just a guess and is usually wrong. And here is where it gets weird. Once they made that jump to the incorrect identification the birders will start saying that they see field marks that are not there, but that are consistent with their jumped to label. Let me say that again. They start seeing things that are not there! How we think about the world alters how we perceive the world. By giving in too quickly to the urge to put labels a thing, we can influence how view the thing. This gets downright dangerous in the world of science.

I would like to encourage everyone (scientists and non-scientists alike) to do, would be to look at an object and really see what it has to show you. The identification of an object is the end goal, not where we should be starting. Instead, the first step must be to make careful observations. Just look at the thing and see what is actually there without making any jumps or judgment calls. Then the information from those observations needs to be carefully thought about. Then, after you have absorbed and considered what is in front of you, let that information guide you to an identification, if possible.

But really see the world! Don’t see what you want to see, or what you think you are going to see, or what you think someone else is expecting you to see. Just let yourself take a moment to look carefully, and really see.

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Spores vs. Gametes

The life cycle of plants is quite different from the life cycle of animals. Plants go through a cycle called alternation of generations which means that there are two multicellular stages. One is diploid, called the sporophyte, and one is haploid, called the gametophyte. In contrast, our animal life cycle has only one multicellular stage, the adult that we are all in as we read/write this.

These two multicellular stages mean that there are a lot of other facets in the plant life cycle that may be unfamiliar to those of us with animal life cycles. The one that I am going to focus on here is the difference between spores and gametes. In dipoid organisms, like us, we have no spores. Our only single cell stage are our gametes. But plants have both spores and gametes and this can lead to some confusion because there are some similarities between the two. Spores and gametes are singles celled, and they are both haploid. But these are pretty much the only similarities you will find.

Fundamentally, spores and gametes are very different. One difference is in the type of reproduction that each are involved in. Spores are used in asexual reproduction, while gametes are used in sexual reproduction. Another difference is in what each needs to develop into the next stage in the life cycle. A spore has the ability to grow into the adult gametophyte all by itself. It does not need to interact with any other cell to do this, all it needs is to find favorable growing conditions. A gamete has to fuse with another gamete before it can form a zygote that then can grow into the adult sporophyte. A third difference is in the life span of these cells. Spores have a very tough outer layer that allows them to remain dormant, but viable, for extremely long periods of time (sometimes decades or even longer) in order to persist through periods of poor conditions until better growing conditions arise. Gametes are much more delicate and generally only remain viable for a matter of days, and so must find another gamete quickly. A fourth difference, related to the how long each cell lasts, is dispersal ability. Especially in more basally derived plant lineages, spores can disperse very, very long distances. They are small and light, and so can be carried by the wind for hundreds, or even thousands, of miles. Gametes, on the other hand can only disperse very short distances. The egg, the larger gamete, is generally retained and so does not disperse at all while the sperm, the small gamete, will swim to find an egg, but will generally only swim a few inches. Yet another difference between spores and gametes is the process by which they are created. Spores are created through meiosis. The structure that produces a spore is diploid and so must go through a process of chromosome reduction in order to create the haploid spores. Gametes are produced by mitosis. The structure that produces a gamete is already haploid and so does not need to change the number of chromosomes it has in order to produce haploid gametes.

So, hopefully this post explains how different spores and gametes are. I wanted to highlight this information because I see it as a common source of error.

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Phylogenetic Vocabulary

As a graduate student, teaching biology labs is a regular part of my week and the lab that I teach most quarters is on phylogenetics and biodiversity.  Recently I have been having discussions about phylogenetic terms with my students, fellow TAs, and the staff and professors who are in charge of the class.  Terminology often gets confusing in phylogenetics, and words are sometimes used to mean different things by different people.  One of the facets that makes these terms extra confusing is that they are not mutually exclusive and depend on the groups being discussed, so for example, a trait can be both a synapomorphy and an autapomorphy (see below) depending on the groups being examined.  So, in an attempt to clear things up in my own mind, and so hopefully be able to teach them more effectively, here are some commonly used terms in cladistics with accompanying definitions and explanations.

Apomprphy – A derived character state.  This is anything that is an innovation along an evolutionary linage.  So anything that is different from the ancestral character state.  For example, within the phylum Chordata, the evolution of a vertebral column, which is something lineages that branched off earlier in Chordate evolution do not have and so is new in the Class Vertebrata, would be an apomorphy.

Synapomorphy – A shared, derived character state.  This is an apomorphy that two taxa share and that is assumed to have been present in the common ancestor of those two taxa.  An example would be feathers in birds.  All birds have feathers, and it is assumed that they have feathers because the common ancestor to all birds had feathers and passed that characteristic down through the generations.

Plesiomorphy – An ancestral character state.  This is any trait that was inherited from the ancestor of a group.  For example, reptiles are exothermic, they do not maintain a constant internal body temperature.  They have this characteristic because the ancestor of all reptiles was exothermic.  This differs from a synapomorphy because some descendants of the first reptiles are not exothermic (birds are endothermic).  In other words, this trait is ancestral, but is shared by some, but not all, of that ancestors; descendants.

Symplesiomorphy – A shared, ancestral character state.  This is any trait that was inherited from the ancestor of a group and has been passed on into more than one descendant lineage.  To carry on with the example for a plesiomorphy, the fact that crocodiles and turtles are both exothermic, but

Autapomorphy – A derived trait that is unique to a particular taxa.  These are not useful in determining how groups are related since only one group will have the particular trait.  However, these are extremely useful in identifying taxa.  For example, feathers only occur in birds.  This makes the character “feathers” and autapomorphy for class Aves.  The character “feathers” is also a synapomorphy for taxa within class Aves.  Raptors and songbirds both have feathers and they inherited them from a common ancestor.

Open circles = ancestral character state, filled circles = derived character state.

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Disappearing Molluscs

The phylum Mollusca is one of the most diverse groups of animals in the world.  It includes familiar organisms, like the snail in our gardens, and not-so-familiar organisms, like the recently discovered Colossal Squid that cam grow to up to 33 ft long and weight 1,100 lbs!  This group is comprised of three major classes the Gastropods (slugs and snails), the Cephalopods (squid, octopus, cuttlefish, nautilus), and the Bivalves (clams, mussels, oysters, scallops).  Several more smaller groups exist as well.  In total, all these groups combined account for about 200,000 living species!  Ecologically, molluscs interact in many complex and important ways from decomposers to predators to prey.

Of the 200,000 species of molluscs, most are marine, but as we all know from everyday lives there are plenty of terrestrial molluscs as well.  At least for now.  Terrestrial molluscs have been experiencing dramatically high rates of extinction in the past half century.  The International Union for the Conservation of Nature (IUCN) publishes a Red List which identifies the conservation status of all species every five to ten years.  The IUCN has identified about 800 in the last 500 years, and of those about 300 are molluscs.  That means that about 40% of all extinctions belong to this one group, and some people have estimated the number of molluscs we have lost to be as much as double the IUCN estimate.

Most of these extinctions have taken place on small oceanic islands which is not surprising.  Ecosystems on oceanic islands are notoriously delicate, and extinctions often occur in response to ecological disturbances such as the introduction of some new predator, the clearing of land for agriculture, or competition with other newly introduced species.  Their fragility makes oceanic islands the canaries in the coal mines giving us early warnings of what might befall continents if we do not stop, or at least slow, the current rates of ecosystem disturbance.  On the Gambier Islands, for example, there were 46 species of terrestrial snail.  Of those 46 species, 43 are now extinct.  Many of them have not even been given names.

An interesting footnote is that while terrestrial molluscs are disappearing disturbingly quickly, marine molluscs are not.  Is there something about the marine environment that makes species that live there less prone to extinction?  Is it just that there have been fewer introduced pests and predators to oceans and to land (since land is where humans spend most of their time)?

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Darwin’s Four Conditions

Charles Darwin (1809-1882) is famous for developing a way for evolution to occur, natural selection.  It should be pointed out that when Darwin was alive there was no question that species evolved.  Scientists in general all agreed that the species that were alive around them did not remain fixed forever and ever, but rather changed over the course of long spans of time.  The problem was that no one could figure out how this took place.  Darwin made observations of the natural world and noticed four simple features that would result in species changing in response to the natural environment.  The process of change that Darwin proposed occurs as an inevitable consequence of these four conditions, and does not require any divine influence.  The four conditions that Darwin elucidated were variation, heritability, superfecundity, and non-random mortality.

Variation means that that each individual in a population is unique.  These differences may be very minor, but they are always there.  This is so obvious a fact that it almost does not need to be spelled out.  You are a unique individual who has never occurred before and will never occur again, and the same is true of every other species.

Heritability means that each individual will tend to pass on the variations it has to its offspring.  In this way, the variations that are present in a population will tend to be passed down through the generations.  In other words, short individuals will tend to have short offspring, etc.  This heritability is not perfect, in most traits, because there is mixing between the traits of each parent.

Superfecundity means that more young are produced than can possibly survive.  Each individual strives to pass its genes on into the future.  To accomplish this, the more offspring produced the better and since all organisms use this strategy, a great many offspring are produced.  This leads to competition among unique individuals for a limited number of available resources needed for life.

Non-random Mortality means that how dies matters.  Many organisms die, and this is especially true of young organisms.  This is driven,in part,  by the competition mentioned above and, in part, by factors such as harsh weather conditions and other environmental factors.  But while it is a foregone conclusion of superfecundity that some individuals will die, it is the fact that these deaths do not occur at random that allows for population-level changes to occur.  In other words, the survivors survive for a reason, and the reason is that they have some advantage, however small, over those that did not survive.  The survivors are then able to pass their advantages, whatever they are, on to the next generation.

After generations and generations of this combination of conditions, populations of individuals become evermore adapted to the environments in which they live, and so evolution by means of natural selection occurs.

 

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Discussing Evolution

To be completely honest, this post is a bit of a tirade on my part.  I have been hearing some views of evolution that have really been annoying me lately.  I am not talking about people who do not think evolution happens or anything like that (that would be a bigger tirade, trust me).  No, these views come from biologist who should know better.  But first, some background.

As a graduate student, I serve as a teaching assistant each quarter.  The most common position I have held is teaching labs for one of the big introductory biology classes that pretty much everyone has to take in college.  Specifically, the labs I teach are part of the class on phylogenetics and biodiversity (BIS 2C for any U.C. Davis people reading this).  While teaching these labs, I have the opportunity to interact with lots of other people who work a U.C. Davis including members of the faculty, administrators, and staff.  Since the class covers the diversity of all life on earth, these people all come from very different academic backgrounds from spider phylogenetics to fungal biology to microbial diversity to botany.  This week we are finishing up plants for the quarter and as part of the plant labs there are several botanists who help the students out.

And here is where my trouble lies.  Several of the botanists have asked students some variation on the following question: why do ferns have fewer herbivores than flowering plants?  This is a perfectly reasonable question.  My complaint comes with the answer that they give which is some variant of: ferns have been around longer and so have had more time to evolve defenses against herbivory than flowering plants. I have so many problems with this answer, I am not even sure where to start!

Now it is true that ferns, which are Monilophytes, diverged from the rest of plants earlier than flowering plants, which are Angiosperms.  As such Monilophytes display more ancestral traits than the more modernly diverged Angiosperms.  However, this does not mean that they have had more time to evolve!  All life on earth can trace its lineage back to a universal common ancestor.  All life.  Since we all started at the same point, every organism that is alive today has been evolving for the same amount of time!  We humans classify different organisms into different group and arrange the formation of these groups into chronological order, but that only indicates that the lineages that make up those groups have changed more or less over the course of the last 3.6 billion years, not that some of them are shorter or longer.

Another reason why this answer gets me hot-under-the-collar is that is reenforces the mindset that some organisms are older than others and therefore more primitive, or less evolved.  Natural selection has been operating on all lineages all the time which means that every organism that is alive today is just as evolved as every other organism that is alive today.  It may sound crazy to say that a single-celled bacteria is just as evolved as a human, but it is true.  The bacteria simply found a strategy for surviving very early on, and that strategy has kept on working really well.  Our ancestors, on the other hand, have had to keep altering their strategy over time to the point where they now look very different from how they did when they started.  Remember that the starting point for both groups was at the same point something like 3.6 billion years ago.  All of phyogenetics basically boils down to tracking which genetic lineages have accumulated what changes over their 3.6 billion year history.  We are all equally evolved!  Or as Neal Stephenson wrote, “Like every other creature on the face of the earth, Godfrey was, by birthright, a stupendous badass, albeit in the somewhat technical sense that he could trace his ancestry back up a long line of slightly less evolved stupendous badasses to the first self-replicating gizmo – which, given the number and variety of its descendants, might justifiably be described as the most stupendous badass of all time.”

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