Evolution

Recently I wrote a piece kind of throwing together the ideas of human evolution and personal genealogy, two things that clearly are ultimately connected because they both come down to simple genetics and who begat whom, but in reality are so separated in time that we cannot properly connect them. But those who accept genealogies and DNA tests for paternity have to accept evolution, because the concepts are the same. Ultimately genes work a certain way and we understand how they work quite well. Evolution is no great mystery or controversy. What is amazing is that Darwin, with no concept of genes, came up with a system that once genes were studied was found to fit very well how genes actually work. Genetics and Evolution started as separate fields, but amazingly the two separate fields merged almost perfectly. To me genealogy is simply what we can see up close of our evolutionary path. Once we get a few generations back, the branches of our ancestry become quite tangled and hard to see...but they are there. And their imprint is in our genes.

Recenly some new developments occurred in studying human evolution that I now want to fit into my previous thoughts on the subject. Slowly it seems like the path of human physical and cultural evolution is being outlined, and I am enjoying each new piece of information.

(cross-posted at Liza's suggestion, from Cocking a Snook!)

Those who can make you believe absurdities can make you commit atrocities.

—Voltaire

Whether or not you ever watched his game show, if you're a Thinking Parent you probably know that the anti-science, anti-human sophistry of Ben Stein is now a movie called "Expelled", on its tightly controlled private propaganda tour prior to its actual "public" opening in the US April 18. [THAT'S DAY AFTER TOMORROW, folks!] My Sunshine State's whole [bible-thumpin'] legislature was invited [to the sneaky preview] but not reporters.

Good catch from Alternet; it appears that the key to understanding God's hand in the universe rests in every humble jar of peanut butter.

Allow me to introduce my own theory of things. That theory would hold this: reasonable proof that God isn't active in the universe could be deduced from the fact that He doesn't occasionally reach down from the heavens, grab certain people by the neck, shake them, and shout "Hey! You! Shut Up Already! You're making me look bad!"

QED. Happy Easter.

UPDATE - CNN story just posted here, with full transcript of statement.
***********

Still watching the live news conference on CNN and thinking it should be required viewing in every school worldwide -- that is, if we do mean to create and preserve real environments that sustain human life by right instead of might.

"Fighting back was simply not an option."
When one is "not equipped for a fight" and reason fails in the face of unhearing, blinded, singleminded Borg-like purpose with superior numbers and ammunition, then Reason itself becomes an unreasonable response forcibly redefined against your will, becoming not an academic exercise but a raw first-rung survival skill, a matter of figuring out who is fit to survive and what it will take.

"We realized that our efforts to reason with these people were not making any headway. Nor were we able to calm some of the individuals down.
It was at this point that we realized that had we resisted there would have been a major fight, one we could not have won, with consequences that would have had major strategic impact. We made a conscious decision to not engage the Iranians and do as they asked.

And even that kind of Raw Reason falters without intelligence, sound information for making wise decisions, and being allowed untwisted, unmanipulated communication within one's one group of fellows and with the real world. Reason stripped, blindfolded and shoved up against the wall to hear the sound of guns being cocked.

In honor of Charles Darwin’s birthday on February 12th, I am posting a series of diaries on Darwin and his theory. My first entry in this miniseries covered the basics of Darwin’s theory of evolution. My second essay described the "Intelligent Deception Lobby." In this essay, I wish to discuss some of the objections that have been made regarding his theory and show how more than 100 years of research have done nothing but bolster or minorly modify Darwin’s theory.

Ever since Charles Darwin first published Origin of Species, many who see his theory as somehow detracting from religion have tried to tear it down. They have pretty much failed from the start and the more we have learned of biology, the more evolution has been supported, if occasionally modified. Interestingly, most objections to Darwin’s original theory were recognized and brought up by Darwin himself in Origin of Species. Far from avoiding or denying potential problems, Darwin approached them head on, giving his hypotheses as to how the problems would be solved over time. In general, his hypotheses have proven quite correct.

There are three particular objections that are often brought up to try and discredit evolution. First there is the problem of the gradual evolution of complex organs, such as the eye. How can random variation acted on by natural selection produce an organ as intricate and complex as the eye? Second there is the problem of intermediate species. If evolution is a slow and gradual process, why do we never see the intermediate species, the “missing links,�? either alive or in the fossil record? These two problems can be called the Problems of Missing Intermediates and can be solved by, in essence, pointing out that a.) intermediates will be rare and rapidly replaced by improved versions, and b.) in reality, intermediates CAN be seen in both instances. I will address these momentarily.

Yesterday's Darwin Day Essay discussed what evolution is all about. Today I want to revisit the foolishness of those who "oppose" the teaching of evolution, the "Intelligent Deception" lobby.

I originally wrote this as I was reading a biography of Darwin and came to the part where the publication of Origin of the Species has produced a huge religion vs. science debate at an Oxford scientific conference. I am struck by how far we came since then only to see reactionary forces pulling us back towards willful ignorance. From the very beginning, right after the publication of Wallace and Darwin’s twin papers and the publication of Origin of the Species soon after, the evidence for evolution has been carefully put together by excellent scientists providing a clear argument, while those opposed have used spurious evidence, misrepresentation of evidence and reliance on the argument that because evolution threatens their faith, it must be wrong. Since those initial publications, the argument for evolution has merely strengthened with the discovery of DNA and an understanding of mutagenesis, the discovery of many “intermediate species�? as fossils and “precursor organs�? to complex organs like the eye in living organisms. Today, the evidence for evolution is overwhelming, though exact details of how it works are still being worked out.

One of the most ironic things about the religion vs. science debate is that many scientists I know are deeply religious whereas many who push for relgion against science know very little about science. I know active researchers who are practicing and believing Catholics, Protestants, Jews, Muslims, Hindus and Buddhists as well as non-believers, agnostics, atheists and people who don't care about religion at all. One friend takes breaks each day to pray to Mecca. Another friend would break off a discussion to daven at the proper times. In short, many scientists see no conflict between science and their beliefs. I suspect those religious reactionaries who DO see such a conflict are less comfortable in their belief than the scientists who are also religious.

This biography of Darwin was already pissing me off, because so many of the issues that SHOULD have been resolved decades ago are still being debated by people who fear science and who feel that reality should conform to their personal belief structure. This anger was, in a humorous way, spurred further by a sarcastic letter in Nature I read recently:

Nature 438, 422 (24 November 2005)

Is the ID debate proof of an intelligent deceiver?

Richard Palmer1

1. Systematics and Evolution Group, Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada

Sir;

In the ongoing debate over whether intelligent design (ID) should be taught as a legitimate alternative to evolution in schools ("Expert witness: the scientists who testified against intelligent design" Nature 438, 11; 2005), I suggest that ID could be presented as an alternative so long as it is always accompanied by a third option: intelligent deception.

This hypothesis proposes that the ID movement is motivated by an 'intelligent deceiver'. Individuals who understand how to debate alternative scientific hypotheses would never intentionally promote religious dogma as science. So an intelligent deceiver must be at work, guiding proponents of ID to sow confusion over valid scientific debate.

To exclude intelligent deception from debates over ID versus evolution could be considered hypocritical on both legal and moral grounds. And if proponents of ID reject the hypothesis of intelligent deception, their objections would be most interesting to hear, particularly the ones that dismiss the deceiver without imperilling the designer.

I think Palmer is right. There are those whose fear of doubt and debate is so great that they WILL do their best to mischaracterize both their own opinion, pretending that their faith is scientific, and the opinion of their opponents to try and sway popular opinion. It seems that Intelligent Design proponents argue things that fit NEITHER the evolutionary nor the biblical model. Now those who say evolution is true but put a deity at its origin are one thing. They are taking a reasonable path. But those who push Intelligent Design into our schools are doing something else. They are taking points of faith and trying to teach them as science. Evolution shows that RANDOM mutations lead to variety within a species, and environmental influences and sexual preferences put selective pressures on a species such that some variants are favored, some are neutrally selected, and some are selected against. Isolation of a population can then lead to different selective pressures on different populations within a species leading to divergence into two species. This basic outline is supported by 140+ years of solid evidence from careful scientific study. Creationism and its bastard child intelligent design do not have such a pedigree.

Science is a very specific process of hypothesis, testing and revision of hypothesis. When a hypothesis is tested, that test has to be able to solidly DISPROVE the hypothesis. Otherwise it is not a valid scientific test. A hypothesis is something you do your best to disprove. If your careful testing is unable to disprove the hypothesis, then that hypothesis is supported by your test. As years go by and many scientists submit a given hypothesis to successive rounds of testing in an attempt to disprove it, the hypothesis gets refined and further supported until it has such robust support from so many tests that we call it a "theory." A theory is not something that is proven. Nothing in science can ever be definitively proven. A theory can merely be so thoroughly supported that further hypotheses can be built upon it with confidence and very accurate predictions can be made from it. Often years later new information comes up that requires further refining of the theory, but the basics remain intact.

Einsteinian physics did not disprove Newtonian physics per se. What it did was radically refine it in such a way that Newtonian physics is still usable for most day-to-day purposes, but Einsteinian refinement is necessary under extreme conditions.

Evolution is no less robust a theory than Einstein's theories. Both have been subject to many tests and retests and refined over the years. Both are so well supported that although we can expect further refinements, we can also accept them as basically facts from which we can construct confident views of our world and build new theories that can hopefully give us even deeper understandings of the universe.

Intelligent Design, like Creationism before it, is not a scientific theory. Both ID and Creationism start with a desired conclusion and attempt to mold existing evidence around that conclusion. Any scientist who did that would fail out of grad school. For this reason alone, ID and Creationism do not belong in a science class except as examples of what is NOT science. When you start from a desired conclusion and try to mold evidence to fit that conclusion, you are not engaging in science. You are merely trying to bolster up a belief without seriously questioning it. A true attempt to combine belief and fact starts with the fact and tunes the belief to the fact, not visa versa. Proponents of teaching ID and Creationism as "alternative theories" to evolution are trying to bend facts to fit belief. They are being intellectually dishonest. The leaders of this movement are, in fact, intelligent deceivers because they are trying to play on people's beliefs to gain followers to push their particular agenda. ID is even more dishonest than Creationism because Creationism is at least true to its belief. ID is a bastardization that attempts to wedge just enough creationism into evolution classes that a door can be opened for teaching Creationism in its full form.

I am biased in this debate. I am a scientist and I am, most of the time, agnostic. But I also am Jewish and I also respect people who have faith. Judaism is a religion where doubt and questioning and arguing are not only accepted, but encouraged. This is best illustrated in the format of the Talmud, the collected commentaries of Rabbis on the Torah (first 5 books of the Old Testament). Each page of the Talmud has at its center a single passage from the Torah. Surrounding this passage in a kind of spiral are commentaries, often contradictory, from several famous Rabbis. No resolution is reached between contradictory commentaries. Rather, the contradictions and the controversy they imply are an integral part of the study and thought of religious Jews. Although orthodox Jews are as dogmatic as any orthodox religious group, they are also welcoming of debate and doubt. So even what religious background I have is going to be open to scientific debate and doubt thrown on religious texts. Few Jews would ever suggest taking the bible literally. That is a Christian invention as far as I am aware. Jews would consider it detracting from the beautiful complexity of the bible to suggest that its word is literal rather than a mixture of history, myth, morality play and allegory.

But our society is currently dominated by those whose belief is so weak that they consider ANY doubt, ANY questioning of the literal word of the bible (which bible? Which part of the bible? In which language?) so threatening that they will break laws and smear reputations just to stop people from even mentioning those doubts and questions. This is nothing new. Scientific progress has always threatened those whose belief is so weak that when facts threaten their beliefs they have to take the side of beliefs. When someone insists on belief over fact how is that different than psychosis?

The Creationism/ID/Evolution "debate" is not a scientific debate. The scientific debate was over long ago, settled in favor of evolution, and has moved on to bigger and better things like determining whether evolution has been continuous or punctuated, whether the evolution of the universe is best described by a point-particle or a string theory, etc. To paraphrase a comment from a Daily Kos reader, the literal interpretation of the bible on which Creationism is based has been long ago disproved by extremely clear data that shows that the Earth is about 4.6 billion years old, rather than the some 10,000 years old that a literal interpretation of Genesis would require. The age of the universe has been shown, but other means, to be even older. The physics used to determine these ages is the same physics that was used to create the atom bomb, airplanes, TV, computers and rocket ships. If our estimates of the age of the universe, predicted by modern physics, are wrong, then it would be impossible for us to have atom bombs or the computers we are using now. Fossil evidence is one strong source of evidence for evolution. We can indeed follow the evolution of species through the fossil record, though with gaps here and there. Evolution has been observed on a small scale using fast reproducing organisms like bacteria or fish that get isolated in separate lakes as a region becomes more arid. Finally, studying the DNA of living organisms gives us good clues to evolution and strongly bolsters the data from fossils and direct observation. The DNA evidence for evolutionary relationships among species uses the same techniques and makes the same basic assumptions as DNA fingerprinting--the closer the relationship between two DNA samples (usually in comparison with a third sample) the more of a match will be observed. DNA fingerprinting in criminology and paternity cases compares DNA from two individuals. Mapping human migrations compares the DNA of two human populations, usually in reference to a third population. Evolutionary relationships are determined by comparing the DNA of two species to a more distant out species. In essence the three techniques are based on the observation that DNA fingerprints more closely match the more related two samples are. To deny the evidence is valid in the evolutionary argument calls into question the validity of DNA fingerprinting. Yet many who oppose evolution based on “faith�? are perfectly happy to put someone to death based on “DNA evidence,�? not realizing the contradiction between these two views.

The scientific debate is over and evolution is as accepted a scientific theory as any theory in scientific history. But our society has backtracked and is now having a renewed debate NOT about science, but about the role of science in society. The debate is not about evolution, which is scientific fact as much as anything is, but is about how society values religion versus science and whether society should favor fact over belief when deciding what to teach in schools.

This debate should not be happening in America. America was founded by students of the Enlightenment, such as Benjamin Franklin, Thomas Jefferson and James Madison. The very people who wrote our Constitution—the basis for our government—were students of science and often engaged in scientific experimentation. They were not religious fundamentalists, by and large, and in fact wanted to avoid the religious dogmas that dominated Europe. Our Founding Fathers had many flaws (racism and sexism, to name but two), but they very clearly saw that religion was a matter of PERSONAL belief and the less that society and religion mixed the better off both would be. Science was seen as a SOCIETAL matter, which the government should encourage in every possible way. Thomas Jefferson funded the Louis and Clark expedition specifically as a scientific endeavor as well as an exploration of new territory. Our Founding Fathers would be horrified by the attempts by the Bush administration to act as the intelligent deceiver, putting belief over fact.

But the Bush Administration and large segments of the Republican Party are indeed playing the intelligent deceiver, deceiving America to get their way. Evolution isn't even their main front, but it is a way in which they can rally people against science. Republicans wrap themselves in Christianity and declare Crusades. In the process they subjugate fact to belief. They suppress scientific evidence showing that global warming is upon us here and now in their belief that what is good for big oil companies is good for America. They suppress evidence that world fisheries are declining in their belief that deregulation of fisheries is a good thing. They suppress evidence for the harmful effects of mercury and arsenic on children in their belief that deregulation of environmental standards is a good thing. They suppress facts about the Iraq War in their belief that it is a Crusade that will make America strong.

Anytime someone puts belief over fact they are someday going to get hit hard in the face by the facts that they ignored. Global warming will hurt America (probably already is!). When fisheries die out, entire industries fail as was seen on the California coast when the sardine (?) canneries collapsed when the fish populations evaporated. America is probably already facing the consequences of industrial poisons in our environment with cancer rates going up and male fertility declining. And, the Iraq war is dragging down America's economy, International reputation and our soldiers who we are sending over there to fight for Bush's beliefs.

America CANNOT be guided by belief over fact. That is not how America was founded. It is a violation of the secular, rational plan that the Founding Fathers had when they wrote the Constitution. It is impractical and intellectually dishonest to, as the Bush administration and the Republican Party have been doing, try and deceive the entire world to push an agenda of faith, whether that faith is in neocon ideology or Christian fundamentalism. Our nation, built to be a place where all religions and beliefs are allowed, was never intended to favor ANY belief over common sense facts.

I call upon Americans to reject the reactionary anti-intellectualism of the Republican Party for a revival of science, common sense and an emphasis on facts. For those who are interested in more on these issues, the Union of Concerned Scientists addresses all of these issues, from evolution to environment to energy issues. The National Center for Science Education and Americans United for the Separation of Church and State focuses on keeping America the secular, rationalist nation that the Founding Fathers intended it to be. Please join in the fight against the Intelligent Deceivers.

This is a reprise of an article I wrote last year in honor of Darwin Day. Enjoy!

Darwin's theory grew out of an era when considerable careful observations from around the world were beginning to be formulated into careful scientific ideas. Not all ideas from this era were equally scientific, nor equally valid. Charles Darwin's theory was formulated based on a huge amount of observation both personally made by Darwin and made by correspondents he wrote to from all over the world. It took many years for Darwin to put his ideas into words and his book, Origin of Species, spends a great deal of time addressing criticisms of the theory of Evolution. When Darwin formulated his theory, the Mendelian rules of genetics were unknown, and DNA wasn't even conceived of. So, in essence, the mechanisms and rules that govern evolution were unknown. Darwin defined the patterns of how living things changed and competed, and it was only later that those mechanisms were discovered, giving the statistical and molecular context for Darwin's theory. Those later discoveries have only strengthened Darwin's theory, never contradicting his ideas.

The most fundamental basis for the theory of evolution is the very simple and very evident observation that individuals within a species vary from one another. This may seem so obvious that it seems silly to state it, but it really is the foundation of Darwin's theory and he spends an entire chapter of his book demonstrating variability within species in nature. We now know that this variation is due to genetic differences, differences in the DNA sequence, among individuals. Darwin did not know this. He simply observed that in every species he had any information on, individuals showed clear differences in appearance, in abilities, in behavior and in internal structures. Simple differences like human skin color or our differences in eyesight are examples of this. What is important about individual variation is that such variations can make an individual better or worse able to survive and produce children. Since producing children is what contributes to the next generation, differences in an organism's chances of surviving and reproducing can determine whether or not that individual organism contributes to the next generation.

There's a thread downstream featuring one of the oldest, and to me most tedious, tropes of American discourse: the fashionably cynical argument that there's no real difference between the two major parties where average folks are concerned. In normal times, this could be dismissed as a modish affectation, the kind that produces the pleasing feeling of being somehow smarter, more in tune with the Zeitgeist, so desired by those who'd like to keep at bay the tedium of making public choices; but these are not normal times. You're just not paying attention, and your argument is akin to doubting the existence of sharks because you haven't been eaten by one yet.

To put it in very stark terms: the foundations of the Republic are under attack. Simply put, while we may have seen precedents for this or that action taken by the former ruling party, we have never, in two hundred and thirty years, seen a systemic assault, on so many fronts at once, on the basic principles of American governance and the civilizational bedrock that underlies them. Once again: among people paying attention, in the academy, legislatures, the bar, business, even the church, this is not a controversial assessment; you, my friend, just haven't been paying attention. And I get impatient with it, because yours is fundamentally a lazy, solipsistic argument.

Thanks to Steam Geek I happened to be looking at the Scientists and Engineers for America website and saw their latest bit of humor:

It is always striking to me that those who speak the loudest about their faith are those who seem to feel that everything is a threat to their faith. To me this in no way illustrates a strong faith on their part, but rather an extremely weak faith.

One of the most ludicrous examples are those who feel threatened by fantasy books like Harry Potter. This issue has come up recently in Georgia schools because a mother with apparently very weak faith felt threatened by this book and wanted it banned. Thankfully the Georgia school board, in this instance, has been more reasonable. From Salon.com:

The Georgia Board of Education voted Thursday to uphold a local school board's decision to leave Harry Potter books on library shelves despite a mother's objections.

The board members voted without discussion to back the Gwinnett County school board's decision to deny Laura Mallory's request to remove the best-selling books.

Mallory, who has three children in elementary school, has worked for more than a year to ban the books from Gwinnett schools, claiming the popular fiction series is an attempt to indoctrinate children in witchcraft.

"It's mainstreaming witchcraft in a subtle and deceptive manner, in a children-friendly format," said Mallory, who is considering a legal challenge of the board's ruling. "The kind of stuff in these books -- murder and greed and violence. Why do they have to read them in school?"