#30 Where do they think snakes came from

This question comes in from Jacob.

The origin of snakes is relatively well researched and has some surprising, at least to me, members of the snake family. I think we should start by defining what makes a snake a snake and then look at the fossil record.

All snakes belong to a clade known as Ophidia which includes snakes and those extinct animals more closely related to snakes than other non-snake squamates (what most people would call lizards are non-snake squamates). Interestingly, more and more evidence is mounting to include members of the Mosasaur family within snakes as they share many characteristics with pythons, more on this later. The appearance of the Ophidia clade is suggested to lie in the early to mid Cretaceous period (145-65 million years ago). Characteristics of modern snakes, but not all snakes, includes scaled skin, limblessness (not entirely true for pythons, boas and extinct species), moderate to extreme extension of the thorax, and decrease in the number of cervical, lumbar and pelvic vertebrae.

Fossil evidence:

Tetrapodophis amplectus from http://www.sci-news.com

Snakes have a somewhat spotty fossil record. Delicate bones and the large number of ribs with a lack of more robust leg bones, or robust skulls leads to the rarity of snake fossils. However, many do exist and allow for significant, if not total, understanding of the origin of snakes. In fact, the earlier mentioned 145 million years ago is in the process of being disproven with a recent discovery in Alberta that may be as old as 167 million years. The skulls of these new species place them firmly in the snake classification. Another fossil, which is younger, Tetrapodophis amplectus, is a four legged animal that has all the body features of a snake in addition to having four limbs. The overlap between limbless fossils and those with two or four legs that all bear the derived anatomy of snakes makes a very tangled picture. However, it is not uncommon to have this kind of variability in the evolutionary process. Though two theories have been hotly debated, burrowing vs marine swimming, the burrowing theory is finding support from CT scans. These suggest snakes lost their limbs to burrow.

Mosasaur from the Oceans of Kansas collection: http://oceansofkansas.com/mus-mosa.html

When snakes have legs...:
Not all snakes, fossil or modern, are limbless. Modern members of the python and boa family have a structure called pelvic spurs. These spurs are remnants of their leg bones, referred to as vestigial structures. I discussed snake legs in a previous post about limbs. Cornell University has a short video about snake toes. Then we have the ancient marine reptiles of the Mosasaur family. Research is building to show that they at least share a more recent common ancestor with snakes than other reptiles while other research suggests that they might in fact be snakes.

So where does that leave us...
Research suggests that snakes evolved from burrowing lizards. Based in the fossil record there seem to be multiple species with legs that possess many of the derived characters that make a snake a snake. This information gives weight to the idea that snakes are evolved from a much earlier lizard which would have had four limbs. These limbs were later lost, mostly, but retained in full, perhaps, by the mosasours and partially until the modern time in the pythons and boids. In reality, scientist are still combing the fossil record and DNA, in the form of comparative genomes, to produce a complete family tree for snakes and their ancestors. Even venom origins are helping paint a better picture of snake evolution.

#28 Book Review: Undeniable: Evolution and the Science of Creation

Undeniable: Evolution and the Science of Creation

By Bill Nye

What is this book about?
This book, despite the title, is actually focused on the basic research, discoveries and theories that support evolution. It discusses the benefits that have come from the study of evolution and the history of the concept.

What I love about this book...

It is written in a very relaxed and informative. It is very easy to read and is written very much like the Bill Nye the Science Guy TV show. The book covers some very in-depth and complex science concepts in a way that anyone can enjoy and understand. It has a lot of humor as well as seriousness. Even as someone who knows the science background there was enough history and related information to keep it interesting.

What could have been better?
This is a book that I read in print and kind of wish I would have listened to the audiobook. I feel like Bill Nye's exuberance that comes through in his voice would have made the book even more enjoyable. I do feel like the title might keep people from reading this book. There isn't much in this book about creationism at all which some people might think given the title.

#24 What is Evolution Part 3 of ? What is meant by natural selection?

Evolution is change over time in its most basic description. The first question seems to be how does that change occur. This is where Darwin's Big Idea comes in... Natural Selection.

Natural selection has four main concepts that define how selection happens. Selection is just a fancy word for the species or varieties or populations that survive and continue on. Natural Selection means that those creatures that are best suited based on these four principles will be "selected" to survive and continue on.

Natural selection works on populations and species as well. It can be affected by interactions of members within the same species (say a cheetah who is faster than its neighboring cheetahs may catch more food and therefore more of its offspring survive) or between different species (say competition between two bird species for insects or the faster zebras leaving more offspring because they are better suited to outrunning predators).

1. Struggle for existence.

- More individuals are produced than can survive. All members of a population or species must compete for food, water, space, mates, etc.

This seems logical when you think about it since the same species is looking for the same food, same nest sites or same territories, etc. So which members survive? The members that are best suited for finding food, evading predators, raising young, catching prey, attracting mates or whatever it may be will leave the most offspring. If you leave more offspring more of your genes and genetic material make it to the next generation.

2. Variation

- Variation exists between individuals in a species or population and this variation plays an important role in the struggle for existence.

There are quite a few examples of how variation is helpful. The classic example is the Peppered Moth. Originally, this moth lived on tree that were mottled and greyish white. The white moths blended perfectly into the bark. However, sometimes black individuals were born. These black individuals were very visible on the white tree trunks and therefore eaten by birds. In this situation the white moths are better suited for the environment than the black... the white are better at winning the struggle for existence.

Enter man and the industrial revolution. With the introduction of coal burning soot began to cover and darken surfaces, including the tree bark. Now the black moths were better suited for hiding and the white moths were easy to find. Birds ate the white moths that they could see on the tree bark. The black moths, due to environmental change, had become better at the struggle for existence.

Currently, with clean air technology and laws the surfaces are once again lighter colored. Guess which moth color is better at surviving now? That's right, the white ones.

Prior to the industrial revolution.

During the Industrial Revolution

#3 Adaptation.

- This is a heritable trait, i.e. something in the genetic code, that increases an organisms ability to survive and reproduce.

Lets play a game... which snake pictured below is the venomous coral snake and which is the harmless milksnake?

Would you want to take the time to try and guess if you knew there was a red, black and white/yellow snake around that could kill you? This is a case of mimicry. The non-venomous snake which had a pattern similar to the venomous snake was avoided. That avoidance means it survived longer and its similarly patterned offspring could survive longer and produce more offspring. This adaptation of looking like a venomous or poisonous counterpart is very common in the animal kingdom. There are many kinds of adaptations mimicry is just one of them.

Oh and if you are curious the second one is the non-venomous milksnake. Would your guess have killed you?

#4 Survival of the Fittest

Before we get into survival of the fittest lets define some words:
Fitness is how well an organism survives and reproduces.
Survival is the ability to pass heritable traits to offspring.

So one way to think about Survival of the Fittest is... Individuals with the best adaptations and variations will be the most successful at the Struggle for Existence. The success will give those individuals the highest fitness and the best survival.

Does this mean that an animal is perfectly suited to its environment or perfect for its environment?  

NO. What it means is that of all the possible variations a species could possess the ones we see most commonly are the best for surviving in the current environment. If that environment changes the types of variations and adaptations needed to survive may change. Some people describe it as "just good enough to flourish". Which means the traits an individual, population or species has is just good enough for that species to flourish, continue surviving, in the current environment. The individual has just enough of an edge on the environment to survive.

So what is Natural Selection really?

Natural Selection occurs when there are heritable traits (variations and adaptations) that cause variations in a population that has more individuals born than are expected to survive. (And this survive here usually means surviving to reproductive maturity.)

This is one of the mechanisms for evolution.

What to try your luck at survival of the fittest? Go here and click on Play the Survival Game.

#23: What is Evolution? Part 2 of ? Who was Darwin?

Before we can talk about the theory of evolution I think it is important to address who the man was.

Charles Darwin was a naturalist who loved bird watching. This is one of the reasons that he often studied pigeons during his research. Most of his observations as a naturalist took place while traveling on ships as the ship's naturalist. Traveling as part of a ships crew was a very common way for scientists to get out and see the rest of the world. Darwin's most renowned voyage was from 1831-1836, at the age of 22, on the HMS Beagle.

Map of the Beagle voyage

 While on this voyage Darwin started to ponder many of the thoughts that would later be worked into the theory of evolution. I am not going to go into great detail on Darwin's notes, he was a copious note taker, however, you can read them Here.


For Darwin, seeing the world and all its inhabitants was life changing.  His big revelation was that biology and evolution can explain how modern organisms evolved over long periods of time from a common ancestor. What we call the Theory of Evolution is all the varied pieces of explanation that Darwin deduced as he tried to figure out how the organisms had changed over time.

Darwin's Theory of Evolution is not one theory but a series of theories and laws that support and give proof for the concept that we call evolution. The theory of evolution includes concepts that we are familiar with, or if you are not we will be addressing in upcoming posts, such as Natural Selection, Mutations, Speciation, and many others. We will get into each of these in the next few posts.



More of Darwin's works:
His Manuscripts
His publications
Creation. This movie is a very good piece of historical fiction about Darwin's work on the Theory of Evolution  
The Movie Creation is currently up on Vimeo to watch in full
Stuff on PBS about Darwin

#22: What is Evolution? Part 1 of ? The Scientists

This isn't an easy question to answer especially if you want to address it in full. Instead of jumping into evolution right away I thought it would be good to start with the scientists and science discoveries that lead up to Darwin's theory and/or whose discoveries were integral to the development of the theory of evolution.

James Hutton (1785)
James Hutton was a geologist who studied Earth processes. He discovered that the Earth's surface was capable of twisting and wearing away. In addition, Hutton proposed that this change was slow and over long periods of time due to activity like volcanic eruptions and rain weathering. He was also the first to think of Deep Time or the concept that the Earth is so old that it is hard (impossible?) for a human to imagine. More on James Hutton, considered the Father of Modern Geology.

Thomas Malthus (1798)
Malthus was an economist that reasoned, if human population grew unchecked that there eventually wouldn't be enough resources to survive. Darwin used this concept heavily in his process of defining how populations might exist over time. More about Thomas Malthus.

Jean-Baptiste Lamarck (1809)
Lamarck was a naturalist who believed that organisms could change during a lifetime by using or not using body parts. His paper on how individuals pass on traits to offspring and facilitating change over time was published the year Darwin was born. Lamarck also thought that organisms had an inborn drive to become more complex. More about Lamarck   and About the difference between Darwin and Lamarck's views on evolution.

Charles Lyell (1830-1833)
Lyell developed the concept of Uniformitarianism. This concept is that the laws of nature are constant over time. What this means is that those events we see now; volcanoes, rivers cutting valleys, erosion, etc must have been occurring in the past. Fun fact: Darwin read Lyell's "Principles of Geology" while on the HMS Beagle. About Charles Lyell and how he came to Uniformitarianism

Question #16: It's not a question at all

I am sure all of you have heard of the Nye vs Ham Debate. If not, you can watch it here on YouTube. Basically the discussion is Evolution vs Creationism, which is valid and in the background I think there is an idea about teaching them in schools, in science classrooms specifically.

Since this debate aired I keep seeing this Post on Buzzfeed with questions creationists would like to have answered. In a spark of inspiration (or possibly insanity) I have decided to tackle these 22 questions. I am not sure if this will be one or two posts. I suppose it depends on how much space they take up. In all honesty, I haven't even read all of the questions before getting the idea to do this.

Question #1: Bill Nye, Are you influencing the minds of children in a positive way?
- I am not Bill Nye so I can not answer for him but I am a science teacher so I will take it in my perspective. As a science teacher I think it is valuable to teach students/children critical thinking, the passion to question everything, search for evidence they can observe and to explore every question that crosses their mind. I think it is positive to teach students how to research and how to determine how valid or strong someone's claim is. Also, myself and you could say Mr. Nye as well, are eccentric in some ways. To show a love of self and not hide the quirks that make us individuals is powerful as well. Most science teachers embrace their passions and encourage their students to do the same. These skills will help them all through life. So, yes, I think I have a positive influence on the minds of the students I teach.

Question #2: Are you scared of a Divine Creator?
-No. In fact I am religious, though not a creationist, and a scientist. I have no fear of a creator. (on a side note, if this is geared toward Atheistic scientists why would they be scared of something they don't think exists? Just a curious counter question.)

Question #3: Is it completely illogical that the Earth was created mature? i.e. trees created with rings... Adam created as an adult.
- In my perspective, yes. I look around and notice that all multi-cellular animals and plants come into being as babies/larvae/seeds. If we look at history we see individuals writing about the birth of baby animals. We can also see baby animals, eggs and tiny skeletons, in the fossil record. This tells me that multi-cellular life, from the beginning, was born as babies of some sort and grew up. I can also observe trees. I see trees sprouting from seeds and gaining rings every year. I can read historical documents about the growth of trees and plants from seeds. I can see seeds in the fossil record, as well as pollen, fruits and flowers, this tells me in the past that trees grew from seeds and gained rings as I observe them growing now. The way nature (development?) progresses has not changed between now and the past.

Question #4:  Does not the 2nd law of Thermodynamics disprove Evolution?
- Nye handles this question in the debate but I will sum it up here very shortly. No. The 2nd Law of Thermodynamics is based on a closed system. The Earth is not a closed system. We get energy inputs from the sun. Gases and heat trickle back into space. Man launches things off the Earth that never return to Earth. "in all energy exchanges, if no energy enters or leaves the system, the potential energy of the state will always be less than that of the initial state." Energy enters and leaves the system we call Earth all the time so this Law is not applied to the Earth.

Question #5:  How do you explain the sunset if there is not God?
-This assumes that I believe that God, as in the Christian deity, created the Earth I live on which is not the case for everyone around the world. Other religions will believe other deities produced the sunset and that God had nothing to do with it or doesn't exist.
- On the science side of things. Sunlight is refracted among the particles of the atmosphere. As the sunsets the light must pass through more particles and shifts from the blues of day to the reds of sunset. The same happens at sunrise. There are many awesome papers out there that describe this phenomenon. Here are a couple.
Layman's version from Science Direct
More in depth from NOAA. With pretty pictures and diagrams

Question #6:  If the Big Bang Theory is true and taught as science along with Evolution, Why do the laws of Thermodynamics debunk said theories?
-First if one science theory is wrong it does not cascade across multiple disciplines causing their theories to be wrong. The Big Bang Theory is a physics/astronomy theory, Evolution is a biological one.
- That aside refer to question #4 for evolution and more explanation. The Universe is also not a closed system. Current science theories are for an ever expanding, visible universe. If it is expanding, it is adding to the system (in this case space) and the system is no longer closed. As mentioned before thermodynamics does not deal with open systems.

Question #7: What about Noetics?
-Noethics is a study of philosophy and not a study of science.What about it? Noethics is not a science discipline and we are talking about science. I don't know what this question is getting at.

Question #8: Where do you derive objective meaning in life?
-This is another question that is not science at all but a question from Philosophy but I will answer it anyway. All over. I see the impact of my person on the well being of others. I feel joy when the sun warms me with all of its radiation and when the sound waves from little Aves shake my eardrums. The significance of my life is defined by how I interact with my world... with my fellow humans. Objective meaning of life is a question of what I find meaningful and what those around me find meaningful regarding my life. I find exploring myself through writing this blog post is meaningful. Others, and myself, find my writing in this blog in general meaningful because they can learn here and ask questions knowing an answer will come. There is plenty of meaning that can be defined without a creator of any kind involved.

Question #9: If God did not create everything, how did the first single-celled organisms originate? By chance?
- That all depends on how you define "by chance". There is an entire branch of science devoted to determining how those first cells formed. This topic is also very heavily studied by Astrobiologists as they try to determine where else in the universe life might evolve. There are some spontaneous chemical reactions that happen which are vital for cells to form. For example, when the lipids (phospholipids) that make up cell membranes are put into water they form membranes due to the interactions between the lipids and the water. One end of the lipid is attracted to water and the other end is repelled by water. These lipids align so that they form balls/membranes. This is also a very in depth topic so here are some sites to learn more.
Berkley and Life Origins
A whole book chapter with diagrams

Question #10: I believe in the Big Bang Theory... God said it and Bang it happened.
-WAIT this isn't even a question. I can't answer it but as a scientist I want this young woman to create an experiment and she and I can do autonomously that tests her hypothesis. When we can both test it through experimentation then we can talk about this as a science question.

Question #11: Why do evolutionists/secularists/humanists/non-god believing people reject the idea of their being a creator God but embrace the concept of intelligent design from aliens or other extra-terrestrial sources?
- There is a flaw in this question as Intelligent Design is a form of creationism. The types of people listed in this question do not believe in creationism and therefore would not believe in intelligent design. So, no, they do not embrace intelligent design from God or extra-terrestrial sources.

Question #12: There is no inbetween... The only one found has been Lucy and there are only a few pieces of the hundreds necessary for "official proof".
- I am not sure what official proof is but there have been hundreds of Hominid skeletons found as well as ancient apes and other kin. This is another topic too broad to handle here so I will leave you with some websites.
The Smithsonian Institute on Human Fossils
Fossil Works has a HUGE database on fossils including many of the Hominid skeletons.

Question #13: Does metamorphosis help support evolution?
- This question assumes all metamorphosis are the same and evolved the same way. This is not true at all. The metamorphosis of a frog, for example, is very different from that of a butterfly. There are mounds of papers on this subject but there is a particularly good one from Scientific American which talks about evolution, metamorphosis and the history of the discoveries surrounding it.

Question #14: If Evolution is a theory (like creationism or the bible), why then is  Evolution taught as a fact?
- First, I never knew the bible was a theory. Can someone explain that part to me? I think what needs to be explained here is the definition of a Theory and how we, as scientists, develop science theories. I am actually going to reference Wiki here because their first paragraph really does a great job at explaining what a scientific theory is.
"A scientific theory is a well-substantiated explanation of some aspect of the natural world, based on knowledge that has been repeatedly confirmed through observation and experimentation.Scientists create scientific theories from hypotheses that have been corroborated through the scientific method, then gather evidence to test their accuracy. As with all forms of scientific knowledge, scientific theories are inductive in nature—that is, they seek to supply strong evidence for but not absolute proof of the truth of the conclusion—and they aim for predictive and explanatory force."

On this basis creationism is not a scientific theory.  Until there is repeatable experimentation and testable hypotheses for creationism it can not be called a scientific theory. Why is evolution taught as a fact? Because repeated experimentation by a vast number of scientists has show that it is the process that lead to the diversity of life forms on the Earth. Creationists would have to develop an experiment that could be conducted by a wide range of scientists that proved that God created diversity. This would be the testing of the hypothesis. If all the scientists involved across a broad range of thinkers came to the same conclusion then Creationism might be a viable theory.

Question #15: Because science by definition is a "theory" - not testable, observable nor repeatable. Why do you object to creationism or intelligent design being taught in schools?
Science is not a theory by definition. Here is the definition of science from several dictionaries: 
Science
noun
1.a branch of knowledge or study dealing with a body of facts or truths systematically arranged and showing the operation of general laws: the mathematical sciences.
2.systematic knowledge of the physical or material world gained through observation and experimentation.
3.any of the branches of natural or physical science.
4.systematized knowledge in general.
5.knowledge, as of facts or principles; knowledge gained by systematic study.
— n
1. the systematic study of the nature and behavior of the material and physical universe, based on observation, experiment, and measurement, and the formulation of laws to describe these facts in general term the knowledge so obtained or the practice of obtaining it

-The investigation of natural phenomena through observation, theoretical explanation, and experimentation, or the knowledge produced by such investigation.  Science makes use of the scientific method , which includes the careful observation of natural phenomena, the formulation of a hypothesis, the conducting of one or more experiments to test the hypothesis, and the drawing of a conclusion that confirms or modifies the hypothesis.
-Thanks to Dictionary.com
 Science is all about testing, observing and repeating. By nature it is all of these things. Theories are part of science but it is not the definition.

Question #16: What mechanism has science discovered that evidences an increase of genetic information seen in any genetic mutation or evolutionary process?
- This is another one of those questions that envelopes several entire college courses. Mutation, non-disjunction, genetic additions or deletions, etc would be likely candidates for some of the mechanisms. Google gave me 58,400,000 selection in half a second on this topic. It seems there are lots of options out there with a search for "mechanisms for genetic additions" I will share some links that I think might answer some of this.
Research Paper on the Genetic Mechanisms that lead to specialized cell types
This is a science heavy explanation of bacterial genetic transfer
Molecular basis of mutations and how that can alter the Genetics

Question #17:  What purpose do you think you are here for if you do not believe in salvation?
-This isn't particularly a science question either.. more philosophy or theology but I will address it anyway. I am here to enrich the lives of those around me, to improve my mind and body, to add to the knowledge and expanse of the human community, to eliminate suffering when I see it, to help others when they are in need, to express compassion, to create beauty in this world.. There are thousands of purposes I have without salvation.

Question #18: Why have we found only 1 "Lucy", when we have found more than one of everything else?
Lucy is the name of a skeleton from the species Australopithecus afarensis. There have been about 300 individual skeletons of this species found. More can be read here on the Smithsonian.

Question #19: Can you believe in the "Big Bang" without "faith"?
- Science is not a faith. Faith is the belief in something that is not based in proof. (again Dictionary.com definition) Since the Big Bang is part of science and science requires proof. Faith and science are mutually exclusive terms.. Science requires proof to believe... faith is belief without proof.

Question #20: How can you look are the world and not believe someone created/thought of it? It's amazing.
- I agree it is amazing. I suppose the other side of this question, the one I want to ask this questioner.. is "The world is amazing. How can you not want to use science to understand how all this amazing stuff works?" This question is more an opinion than a real question.

Question #21: Relating to the Big Bang Theory... Where did the exploding star come from?
-There is a science based problem with this question... at the time of the Big Bang there were no stars. The Big Bang and the development of the universe is a huge topic, too huge to talk about here though it is one of my favorite astronomy topics (next to Black Holes). NASA and BBC Bitesize have some great intro articles on the topic. Also love this poster. Also, any of the books by Stephen Hawking will discuss this in depth.

Question #22: If we came from monkeys then why do we still have monkeys?
-This is based on the misconception that evolution is a straight line..This picture is the culprit in this problem. For years this was the image of human evolution. This is an oversimplified and false representation. This is a more accurate representation. Or even this simplified one. It is a branching pattern. Some branches make it to current day like modern humans, gorillas and howler monkeys. Other branches terminate before the modern times meaning they have gone extinct. All of this is based in a scientific practice/field called phylogenetic studies. Understanding phylogenies will help answer this question. I suggest Berkley and Another Berkley with a cool walk through exploration design. and A basics of the concepts here.


If there are anymore questions about these topics, want me to go more in depth? Send me a message and I will address your science questions.