Tag Archives: Evolution

The Three Necessary and Sufficient Conditions of Natural Selection

Natural Selection is the key creative force in evolution. Natural selection, together with specific histories of populations (species) and adaptations, is responsible for the design of organisms. Most people have some idea of what Natural Selection is. However, it is easy to make conceptual errors when thinking about this important force of nature. One way to improve how we think about a concept like this is to carefully exam its formal definition.

In this post, we will do the following:

  • Discuss historical and contextual aspects of the term “Natural Selection” in order to make clear exactly what it might mean (and not mean).
  • Provide what I feel is the best exact set of terms to use for these “three conditions,” because the words one uses are very important (there are probably some wrong ways to do it one would like to avoid).
  • Discuss why the terms should be put in a certain order (for pedagogical reasons, mainly) and how they relate and don’t related to each other.

When you are done reading this post you should be able to:

  • Make erudite and opaque comments to creationists that will get you points with your web friends.
  • Write really tricky Multiple Choice Exam Questions if you are a teacher.
  • Evolve more efficiently towards your ultimate goal because you will be more in control of the Random Evolutionary Process (only kidding on this third one…)

Continue reading The Three Necessary and Sufficient Conditions of Natural Selection

A short list of banned books

To Kill a Mockingbird*
The Hate U Give*
The Color Purple: A Novel*
The Absolutely True Diary of a Part-Time Indian*
Stamped: Racism, Antiracism, and You: A Remix of the National Book Award-winning Stamped from the Beginning*
The Catcher in the Rye*
The Autobiography of Malcolm X: As Told to Alex Haley*
I Know Why the Caged Bird Sings*
The Lord Of The Rings Illustrated Edition*
Persepolis: The Story of a Childhood (Pantheon Graphic Library)*
Slaughterhouse-Five: A Novel (Modern Library 100 Best Novels)*
The Handmaid’s Tale*
Hop on Pop (I Can Read It All By Myself)*
Lord of the Flies*
1984*
The Giver (Giver Quartet, 1)*
Lawn Boy*
The Diary of a Young Girl: The Definitive Edition*
Harry Potter and the Sorcerer’s Stone*
The Complete Maus*
Lolita*
The Glass Castle: A Memoir*
Fahrenheit 451*
Out of Darkness*
Critical Race Theory (Third Edition): An Introduction (Critical America, 20)*
And Tango Makes Three: Book and CD*
Assata An Autobiography*
The Kite Runner*
The Handsome Girl & Her Beautiful Boy*
The Pentagon Papers: The Secret History of the Vietnam War*
A Civic Biology: The Original 1914 Edition at the Heart of the “Scope’s Monkey Trial”*
The Bluest Eye*
Jack of Hearts (and other parts)*
All Boys Aren’t Blue: A Memoir-Manifesto*
Impending Crisis of the South “Annotated”*
Animal Farm*

One Iguana Two Iguanas: Children’s evolutionary biology book, with lizards!

The land and marine iguanas of the Galapagos Islands are famous. Well, the marine iguanas are famous, and the land iguanas, representing the ancestral state for that clade of two species, deserve a lot of credit as well. The story of these iguanas is integral with, and parallel to, the story of the Galapagos Islands, and of course, that story is key in our understanding of and pedagogy of evolutionary biology, and Darwin’s history. Continue reading One Iguana Two Iguanas: Children’s evolutionary biology book, with lizards!

How to choose the sex of your baby.

In order to make such a momentous decision, I insist that you learn the very interesting evolutionary biology behind it.

Start with this paragraph:

But for modern medical science, a baby’s sex would remain unknown until birth. But many mothers today know long beforehand whether a baby will be male or female. Routine ultrasound scans reveal fetal genitals a third of the way through pregnancy, and genetic tests identify sex even earlier. Yet basic questions remain. Is a baby’s sex like coin tossing, or can the male:female ratio be skewed? If sex bias occurs, does it happen through sperm sorting before fertilization or mortality differences in the womb after conception?

Then, CLICK HERE to read the rest of the story, by Robert Martin, expert on such things.

The Early Bird Crushes The Egg

Model I birds, the kind that lived during the Age of the Other Dinosaurs, may not have brooded their eggs. Today, birds sit on their eggs in such a way that the adult bird’s down surrounds the ovoids, and warmth from the adult can keep the eggs at a constant temperature. Depending on the bird, you may find additional intersting adaptaitons. For example, Penguins use their own feet as a nest, placing the egg there. One adult broods the egg for a long period (days, in some species) and then swaps with the other adult, with the swapping being very ritualized in some cases. Like this egg swqap between parent Adelie penguins (Tip: this video does not show the actual swap): Continue reading The Early Bird Crushes The Egg

Sexual Selection Up To Date: A Taste for the Beautiful

A Taste for the Beautiful: The Evolution of Attraction is a popular science book written by an actual expert on the field, addressing the ways in which the world of animals is shaped by sexual selection.

One of Darwin’s major contributions to the panoply of theoretical and observational work we call “evolution” was to recognize, describe, and model sexual selection. Continue reading Sexual Selection Up To Date: A Taste for the Beautiful

Darwin Quotes, Assembled

From Janet Browne, the author of Charles Darwin: A Biography, Vol. 1 – Voyaging and other works about Charles Dawin, The Quotable Darwin.

Quotes by Charles Darwin are not just the stuff of memes. Even the fake quotes. They can be the center of long arguments, or at least, they can significantly augment the arguments. For example, did you know that while Darwin never used the term “missing link” he did talk about missing links quite a bit, missing links are central to his thinking about evolution, and all those writers of today who claim that we must never speak of missing links are misguided? Continue reading Darwin Quotes, Assembled

ALERT: Two very good deals on two very good books

Every single regular reader of this blog has read or intends to read Stephen Jay Gould’s The Panda’s Thumb: More Reflections in Natural History. I just noticed that the Kindle version of it is available for $1.99, and I assume this is temporary. I already had the book on dead-tree matter, but I picked this up because ebooks are searchable! You will want one two.

Every single regular reader of this blog SHOULD want to read, or should have already read, Mary Doria Russell’s excellent binary set including The Sparrow: A Novel and Children of God. (The Sparrow is first, COG second.)

Right now, and I assume very temporarily, The Sparrow is also avaialble for $1.99.

A quick word about the Sparrow series. It has been classified as science fiction. Others have said, no, it is not science fiction, it is philosophy and spirituality. A lot of church groups read it because of its religious meaning and implications.

That is really funny because there isn’t a drop of religiosity in this series. There is a priest, but it is a priest mainly operating in a post-religion world. This series is primarily anthropology fiction, which happens to be set in a science fiction theme, and if anything, it deconstructs the central role of religious institutions and makes them look as potentially lame and potentially nefarious and as potentially impotent as the other institutions. Or, really, as products of human behavior as anthropologists understand it, the outcome of a mix of self interested behavior, bonding or revulsion, racism and in-group vs. out-group thinking, the power of institutions, ritual, tradition, class, and exploitation. Set, of course, in the background of co-evolution of morphology of predator and prey. There is also a linguistic theme addressing meaning creation (or lack there of: ouch), development of mind and behavior, language learning, and so on.

You have to read them, and now you can get one of them for two bucks! (Unfortunately COG seems regular price.)

Let me add this too, just noticed it, could be of interest for two bucks: The Science of Star Wars: The Scientific Facts Behind the Force, Space Travel, and More!.

Universal remotes, evolution, sex, and sight

So Amanda had this TV. It had a remote. The remote sucked. It was broken. Then I moved in and with me came a universal remote. Lucky Amanda. I programmed the universal remote (a Radioshack 5 in 1) to handle the TV as well as a DVD player and a stereo. The remote handled everything. The old remotes hung around for a while occasionally being used, but then disappeared. Then we got a different DVD player and I had forgotten that the remote was a universal jobbie, so we just started using the remote for the DVD player Then we got an iPod cradle with speakers and a Roku. I purchased a Radio Shack switchbox during the Creation Science Fair at Har Mar in 2010 (some of you will remember that i did that, I was showing off a bit.) I ran the Roku to the TV via the switchbox. I ran the new DVD to the TV with the switch box. I got rid of the stereo (it was 99 percent broken). The switchbox was necessary because of the lack of connectors on the TV. While I was doing that, I also ran all of the audio outputs to the iPod cradle. And there was a Wii, so that ran through the switchbox to the TV as well as the iPod cradle.

So we had a TV remote that was originally a universal remote, but we forgot that it was a universal remote. We had a DVD remote. We had a Roku remote. We had a remote for the iPod cradle. We had a switchbox which was not have a remote but was kinda like a remote.

So…
Continue reading Universal remotes, evolution, sex, and sight

Understanding Michele Bachmann in the context of Human Evolution

The only thing harder to understand than Michele Bachmann is the Republican Party. Bachmann is hard to understand in this way: How can a person with her mind be an elected member of congress? The Republican party is hard to understand in this way: How can a party that is trying to become more rather than less relevant keep putting Michele Bachmann on the podium in places like the National Party Convention and, most recently, at CEPAC?

I can’t explain any of this, but I can at least redescribe the problem in reference to a theoretical construct for the evolution of the human mind. I endeavor to do this for three reasons: 1) To have a chance to briefly discuss these theoretical ideas; 2) To try to place Michele Bachmann and the Republicans (and by minor extension, by the way, Sarah Palin) in at least a descriptive, if not explanatory, context; and 3) because I get to use the word “meta” a million times throughout this essay. No, no, not really. The third reason is because I feel this nagging need to make the link between the fact that Michele Bachmann should not be in Congress with the fact that not only is she actually in Congress, but was recently re-elected to congress. Specifically, I will assert that there is not always cognitive dissonance where one thinks one sees it. Michele Bachmann was re-elected because she represents the majority of her constituents quite effectively.

There is a theory that what makes a good story is meta-osity. A story about a person and another person interacting is too simple. A story like this but where one of the people is secretly manipulating the interaction is a bit interesting. A story like this but where, unknown to the manipulator, there is a larger scale manipulation going on is a novel that might sell. And so on.

There is another theory that presumes this first theory to be essentially correct, and that the human mind is actually an evolved organ designed to manage these meta-meta-meta states. The reason for this is that much of the important stuff in life is meta-meta. Ultimately, in a human society where food- and sex-competitive apes are violating the basic tenets of competition by living side by side and cooperating and sharing within groups, reproduction and survival are socio-political meta-meta matters.

My personal “belief” (read: informed hunch) is that this is essentially true, but the proximate mechanism for the human mind being able to do this is a pretty simple (yet biologically costly) genetically mediated neuro-developmental process overlapping with and followed by a culturally and experientially mediated neuro-developmental process, with a large part of that arising during the unique (compared to other apes) human developmental phase we all “childhood.” (See The Symbolic Species: The Co-Evolution of Language and the Brain by Terry Deacon for a run down on this approach.)

Which leads me to Michele Bachmann, who recently said:

I just wondered that if our founders thought taxation without representation was bad, what would they think of representation WITH taxation?

Uffda. To put this in context, just spend a minute and a half reviewing this speech at CPAC:

[sorry to report, this speech seems to have disappeared from the internet]

OK, well, putting it in context didn’t help, did it? But along side the other statements made here and elsewhere by Bachmann, we are starting to see a pattern.

You know about Michel Bachmann’s other problems. The Blue Scare scenario comes to mind. Bachmann called for the investigation of all elected Democrats in the federal system for Unamerican-ness. If you don’t agree with me you must be the enemy, and I must fear you. All of us who fear you must treat you all the same and throw bricks at you, as children might do. And so on.

Now let’s talk about what all this means. Bachmann’s statement (above) about taxes is an example of not understanding even the first level of meta, the most basic nuance, of the original slogan. Bachmann’s placement of all people who disagree with her in the same category, so that enemies and colleagues of a different party are all the same, is an example of the inability to go beyond the most basic of relationships. Bachmann is unable to see that we can disagree with our colleague, but join our colleague to disagree with a third party (meta) and sometimes ally with a third party to disagree with yet another third party (meta meta) and sometimes find influence among allies in a distant third party to effect change in a colleague (meta meta meta).

(By the way, that this analysis is valid is underscored by Bachmann’s insistence that actual card-carrying Republicans who happen to disagree with her are not “real” Republicans.)

Bachmann does not get even the simplest nuance. In politics, she is just a dog barking at the shadows behind the fence, and everything is a shadow behind the fence.

We can show that many animals including dogs have this level of capacity and not much more. A meta-X level, where you have one set of complexities on top of basic relationships, is clearly a generalized primate capacity and may even be found in some social birds, but is not well developed in dogs or other carnivores.

The next level of meta … meta-meta-x … is probably exclusively human, and if Homo erectus was around today, perhaps we’d be saying “Oh, H. erectus can do that. Sort of.” (I’m guessing at that.)

Beyond this, the next level of meta … meta-meta-meta-x … is what most humans can do when they try and have certain experience or training, and that very smart people do a lot of, and real smart people are probably doing all the time. Most people probably achieve meta-meta-X much of the time, but probably mainly in regards to certain aspects of their life but not others. (Again, I’m guessing.) Meta-osity is a general feature of thought and thus could be conceived of as independent of empirical realities, but I don’t think this is the case. I think there is a real relationship between physicality and thought process. So a person may be meta-meta-X or even meta-meta-meta-X about the novels they read and their family relationships, but little else. A different person may be meta-meta-meta-X about their workplace relationships and the stuff they do as an engineer, or teacher, or crane operator, but be meta-X at best when it comes to politics. And I think, in fact, that this is exactly what frequently happens. It may be in the interest of certain politicians to keep the conversation at a meta-X (or lower) level.

Ideally, in careers, and especially careers that are important to other members or elements of society, we would like to see people be at least meta-meta-X, especially those in charge of important things. For example, physicians should be meta-meta-meta-X, if possible, regarding the workings of the body in relation to disease, personal behavior, treatment options, and so on.

Examples of meta-meta-meta-X thinkers in politics include Bill Clinton, Barney Frank, Newt Gingrich, Adlai Stevenson and Al Franken. One imagines Ted Kennedy, clearly a meta-meta-meta-X thinker, relaxing by sailing on Nantucket Sound, where to succeed he merely needs to achieve meta-X thinking regarding winds, currents, sails, and ropes. Meanwhile, the captain of the Nantucket Ferry, who in her job driving a modern ship rarely has to go beyond meta-X, enriching her own life by engaging in BBC style crime dramas on TV and playing chess with her buddy the Harbor Master in Harwich Port.

Examples of meta-meta-X political thinkers who did well because they were in the right place at the right time might include George Bush Senior, Harry Truman, and George Washington. Examples of meta-X thinkers who probably didn’t apply the meta to the X in their political lives might be …. Hmmm, hard to come up with too many examples of this. Most people at that level would never get far beyond student council. Let’s see, who would be a good examp…

Oh,right, how could I forget!?!? … Michele Bachmann!

Here’s the thing. The objective of a politician might be to manage the thinking of others such that you get those other people to do what you wish them to do: fund your campaign and vote in your favor. It is much much easier to do this if you keep the public level of discourse as meta-free as possible. Newt Gingrich is on my list of meta-meta-meta-X thinkers, but he was a master at engendering the populous with a penchant for non-meta reasoning. For example, Gingrich successfully gained support from the masses by promising to bring to the floor a vote on each of ten allegedly key Republican issues (the famous “Contract with America”). However, a) the House (where Gingrich promised to do this) has weak rules for bringing something to vote, and b) bringing something to vote does not equal passing it or, really, even actually voting on it. So, you see, it would be trivially easy to keep this “contract.” It was not logical to infer that the Contract with America was a meaningful political construct that would have real results, but it became an effective rallying point for the first midterm election during Clinton’s first term. The Contract with America was a dog barking at a shadow behind the fence and nothing more. (Expect this dog to be barking again in about a year from now.)

The re-casting of stakeholders in a given issue as “taxpayers” is often a de-meta-fication of the issue at hand. The conflation of 1960s radicalism with 21st century terrorism with being black, or being a democrat, or being from Chicago, or whatever, is de-meta-fication of a person’s (Obama’s) entire career and philosophy. Claiming that the fact that Soviet/Russian bombers would fly over Alaska on their way to bomb the rest of America makes the governor of Alaska a foreign policy expert is the de-meta-fication of so, so many things.

Years of training have converted much of the Republican base to a pack of dogs, chained to an ideological stake in a dusty gloomy yard, always ready to bark at the movement of shadows beyond the tall fence that surrounds them. Michele Bachmann’s congressional district is demographically as close as any district can be to this Republican ideal. This is why Bachmann can be who she is, get re-elected, and continue to be invited to speak at major Party gatherings. Michelle Bachmann is not Newt Gingrich. She does not grasp the overarching strategy. She is not a simpleton’s face hiding a brilliant political mind. She is just the simpleton. I doubt she is even taking marching orders from anyone. Michele Bachmann is merely one of the dogs, among many, barking at the shadows moving behind the fence.

Michele Bachmann is the best possible representative for her district.

Woof.

The Origin of the Chicken

From whence the humble chicken? Gallus gallus is a domesticated chicken-like bird (thus, the name “chicken”) that originates in southeast Asia. Ever since Darwin we’ve known that the chicken originated in southeast Asia, although the exact details of which one or more of several possible jungle fowls is the primal form has been debated. The idea that more than one wild species contributed to the early chicken has been on the table for a long time, though perhaps not as long as the chickens themselves have been on the table

Notice the yellow legs on this chicken. If you pluck out the feathers, you’ll notice that the skin is yellow as well. But if you go find, say, a crow, and pluck its feathers, it will be grayish in color. Or maybe black, I don’t know, it’s been a while since I’ve defeathered a crow. The point is, that some birds are yellow, some are not.ResearchBlogging.orgThere is a gene that is expressed in certain tissues that produces an enzyme that cleaves the carotenoid molecules that provide the yellow color. If there is no functional copy of this gene (if the individual is homozygotic for the broken version) then this cleaving does not happen, and you get a yellow bird (depending on other factors we shall ignore).In short, new research confirms as previously thought that the red jungle fowl (Gallus gallus) is ancestral to the modern chicken, as Darwin suspected. But this research also suggests that another bird, the grey jungle fowl (Gallus sonneratii) also contributed to the chicken’s genome, providing the yellow color we see on this chicken’s legs.The research, reported in PLoS Genetics, gives us two results. One is the first characterization of the process of pigmentation mentioned above, and the second is a new family tree for this bird.

Many bird species possess yellow skin and legs whereas other species have white or black skin color. Yellow or white skin is due to the presence or absence of carotenoids. The genetic basis underlying this diversity is unknown. Domestic chickens with yellow skin are homozygous for a recessive allele, and white skinned chickens carry the dominant allele. As a result, chickens represent an ideal model for analyzing genetic mechanism responsible for skin color variation. In this study we demonstrate that yellow skin is caused by regulatory mutation(s) that inhibit expression of the beta-carotene dioxygenase 2 (BCDO2) enzyme in skin, but not in other tissues. Because BCDO2 cleaves colorful carotenoids into colorless apocarotenoids, a reduction in expression of this gene produces yellow skin. This study also provides the first conclusive evidence of a hybrid origin of the domestic chicken. It has been generally assumed that the red junglefowl is the sole ancestor of the domestic chicken. A phylogenetic analysis, however, demonstrates that though the white skin allele originates from the red junglefowl, the yellow skin allele originates from a different species, most likely the grey junglefowl. This result significantly advances our understanding of chicken domestication.

Here is the phylogenetic tree that the authors of this paper present:i-a782d8d10ab087febef2b5b4a719fe02-chicken_tree.jpgClick here for a much larger image (84kb)You will read in press reports that “Darwin got it wrong” when it comes to chickens. Let’s have a look at what he said and see how wrong he was. Darwin addressed the two major theories of his time. One is a multiregional theory, much like the now discredited version of human evolution, where each kind of chicken was domesticated from a different wild form. The other is that all descended from one ancestor, Gallus gallus bankiva, also known as Gallus bankiva.Darwin uses chickens in a big way in developing his ideas about evolution. Chickens were perhaps as important as pigeons for examining breed characteristics. Therefore, he wrote quite a bit about chickens. In the end, he favored the single origin hypothesis, but he also describes the primordial species of his choosing … the red jungle fowl … as much more diverse in character than it is generally characterized today…

… Gallus bankiva, has a much wider geographical range than the three previous species; … This species varies considerably in the wild state. Mr. Blyth informs me that the specimens, both male and female, brought from near the Himalaya, are rather paler coloured than those from other parts of India; whilst those from the Malay peninsula and Java are brighter coloured than the Indian birds. I have seen specimens from these countries, and the difference of tint in the hackles was conspicuous. The Malayan hens were a shade redder on the breast and neck than the Indian hens. The Malayan males generally had a red ear-lappet, instead of a white one as in India; but Mr. Blyth has seen one Indian specimen without the white ear-lappet. The legs are leaden blue in the Indian, whereas they show some tendency to be yellowish in the Malayan and Javan specimens. In the former Mr. Blyth finds the tarsus remarkably variable in length. According to Temminck20 the Timor specimens differ as a local race from that of Java. These several wild varieties have not as yet been ranked as distinct species; if they should, as is not unlikely, be hereafter thus ranked, the circumstance would be quite immaterial as far as the parentage and differences of our domestic breeds are concerned. The wild G. bankiva agrees most closely with the blackbreasted red Game-breed, in colouring and in all other respects, except in being smaller, and in the tail being carried more horizontally. But the manner in which the tail is carried is highly variable in many of our breeds,…(Darwin 1868:233)

What we see here (my emphasis added) is evidence that skin color varied across different populations of this species.The study at hand asserts:

On the basis of observed character differences and cross-breeding experiments, Darwin concluded that domestic chickens were derived solely from the red junglefowl, though this was later challenged by Hutt [1], who stated that as many as four different species of junglefowls may have contributed to chicken domestication. Molecular studies of mtDNA and retroviral insertions have supported Darwin’s view. A study that analyzed both repeat nuclear elements and mitochondrial sequences found evidence that grey and Ceylon junglefowls may hybridize with domestic chickens, but did not provide evidence that these two species have contributed to chicken domestication. To date, no studies have compared gene sequences associated with a specific phenotype found in domestic chickens across numerous wild junglefowls and domestic breeds….We searched for the causal mutation … This analysis revealed a surprisingly high sequence diversity between the two groups (0.81%), well above the genome average for chicken (~0.5%) [15] and approaching the sequence divergence between chimpanzee and human (1.2%). We therefore included three other species of junglefowls in the sequence comparison: grey (G. sonneratii), Ceylon (G. lafayetii), and green (G. varius) junglefowls. This step was also motivated by the fact that grey and Ceylon junglefowls have red or yellowish legs which implies deposition of carotenoids and a Y/Y genotype…In contrast, mtDNA sequences from the same samples showed the expected pattern in which domestic chickens cluster with red junglefowl within a clade well separated from other junglefowls

The grey and red jungle fowl have, at present, disjunct ranges, but that may be a product of recent ecological changes, including human alterations of habitats. Also, in the early days of chicken domestication, there is no reason to suspect that a single origin would be followed by immediate isolation from wild forms, and in fact, all the available evidence including that reported here suggests the contrary.I think the truth of the matter is that Darwin did not really get the origin of the chicken wrong … he had it substantially right. Rather, Darwin had a better idea of variation in the wild forms than we may appreciate today, and he leaned a bit more towards a simpler history at the start than we tend to today. That’s not bad considering that all of the modern theory about origins of domesticated forms post dates, and often derives from, Darwin.In other words, Newton understood gravity, so today we can design an airplane. But if Newton designed and airplane that did not fly, would that mean that he got gravity wrong?I think not.


(More on Darwin here)Darwin, C. R. 1868. The variation of animals and plants under domestication. London: John Murray. First edition, first issue. Volume 1.Eriksson, J., Larson, G., Gunnarsson, U., Bed’hom, B., Tixier-Boichard, M., StrÃ?¶mstedt, L., Wright, D., Jungerius, A., Vereijken, A., Randi, E., Jensen, P., Andersson, L., Georges, M. (2008). Identification of the Yellow Skin Gene Reveals a Hybrid Origin of the Domestic Chicken. PLoS Genetics, 4(2), e1000010. DOI: 10.1371/journal.pgen.1000010

Darwin and the Voyage: 10 ~ Rheas and the Birth of Evolutionary Theory

Everyone knows about Darwin’s Finches, of the Galapagos Islands. But of course, Darwin made observations of birds throughout his travels on The Beagle. Here, I present a number of passages from The Voyage that include some of these observations. Continue reading Darwin and the Voyage: 10 ~ Rheas and the Birth of Evolutionary Theory