Here's a figure from a paper by Marques-Bonet et al. (2009). It shows the differences between various human genomes (blue); between the human and chimp genomes (red); and between the human and macaque genomes (yellow).
The results are plotted a a fraction of sequence identity. (Convert to percent by multiplying by 100.) The window is 100 kbp (100,000 bp). Human chromosome 2 is on top and chromosome 7 is below.
Notice that the substitutions are pretty much randomly scattered over every part of the two chromosomes. The data is consistent with the idea that most of the DNA in those chromosomes is junk and most of the substitutions are nearly neutral mutations fixed by random genetic drift. The differences between each pair of species is consistent with an approximate molecular clock corresponding to a constant mutation rate over million of years. The absolute levels of sequence identity (i.e. 98-99% for chimp/human) is consistent with the time of divergence from a common ancestor based on the fossil record and other criteria.
Here are my questions. Is there any other explanation that accounts for the data? Is it possible to explain the results as adaptations—substitutions that are mostly fixed by natural selection? Is it possible to explain the results according to Intelligent Design Creationism?
I'm particularly interested in hearing from the creationists. What is your explanation?
Marques-Bonet, T., Ryder, O.A., and Eichler, E.E. (2009) Sequencing Primate Genomes: What Have We Learned? Ann. Rev. Genomics Hum. Genet. 10:355-386. [doi: 10.1146/annurev.genom.9.081307.164420]
This post was prompted by a discussion I'm having with Jerry Coyne on whether he should be trying to censor university professors who teach various forms of creationism.
I very much enjoyed Jerry Coyne's stance on free speech in his latest blog website post: The anti-free speech police ride again. Here's what he said,
This post is a response to a question posed by Vincent Torley, "Is Larry Moran a conspiracy theorist?"
A few weeks ago the Toronto Star (Toronto, Ontario, Canada) published a front page article on the dangers of Gardasil, a vaccine against human papillomavirus (HPV) that's recommended for adolescent girls. The article highlighted a number of anecdotal stories about girls who had developed various illnesses and disabilities that they attributed to the vaccine. The reporters thought this was evidence that the vaccine had serious side effects that were being covered up by the pharmaceutical industry.
Almost every scientist who read the story recognized that correlation does not mean causation and that the "evidence" promoted by David Bruser and Jesse McLean was no different than the claims of Jenny McCarthy and her supporters about the MMR vaccine and autism. There were dozens of health professionals and scientists who criticized the article in the Toronto Star culminating in a op-ed article that clearly pointed out all the flaws in the original piece [Science shows HPV vaccine has no dark side]. That article was signed by 63 scientists and physicians.
This morning I was flipping through the pages of the week's issue of Nature to see if there was anything interesting. There was. I'll tell you about it later, maybe.
I kept flipping. I found a paper with an intriguing title "New genetic loci link adipose and insulin biology to body fat distribution" [doi:10.1038/nature14132]. The authors found 68 loci in the human genome that are statistically correlated with excess body fat. That's not very interesting because very few of these association studies pan out in the long run. Most of those 68 loci are probably genetic noise.
The end of the paper was somewhat interesting. There seemed to be a lot of authors and affiliations. Let's count the authors 1,2,3,...401! There are 401 authors on this paper and they work at 300 different institutes and universities. The list of authors and affiliations take up three pages in the print edition of the journal!
The next paper has a similar title, "Genetic studies of body mass index yield new insights for obesity biology" [doi: 10.1038/nature14177]. The authors found 97 loci correlated with body mass index (BMI). These loci accounted for ~2.7% of BMI variation.
Not interesting.
There are a lot of authors on the second paper as well. Let's count them: 1,2,3,.....481! There are 481 authors from 347 institutes and universities. The list of authors and affiliations covers almost four pages (!) in the print edition of the journal. Is this a record?
It gets worse. In both lists of authors there are entries under "T" like "The PAGE Consortium" and others. They are marked with double daggers and the footnotes say "A list of authors and affiliations appears in Supplementary Information."
I checked it out. For the second paper there are about 800 additional scientists listed as members of the various consortia.
Am I the only one who thinks this is ridiculous?
How could the seemingly identical sulfur-cycling anoxic sediment-inhabiting biotas of the ∼1.8-Ga Duck Creek and ∼2.3-Ga Turee Creek cherts, like those of Proterozoic stromatolitic cyanobacteria (6, 8), have evidently remained fundamentally unchanged over billions of years?
We suggest differing answers for these two early-evolved hypobradytelic lifestyles:
i) For cyanobacteria, the answer evidently lies in a genetically encoded ecological flexibility derived from their early adaptation to geologically exceedingly slow changes of the photiczone environment (e.g., of solar luminosity, UV flux, day length, and CO2, O2, and usable sulfur and nitrogen). Because of their large population sizes, global dispersal by ocean currents and hurricanes, and capability to generate oxygen toxic to anaerobic competitors for photosynthetic space, these ecologic generalists adapted to and survived in a wide range of habitats (6).
ii) Once subseafloor sulfur-cycling microbial communities had become established, however, there appears to have been little or no stimulus for them to adapt to changing conditions. In their morphology and community structure, such colorless sulfur bacteria—inhabitants of relatively cold physically quiescent anoxic sediments devoid of light-derived diel signals and a setting that has persisted since early in Earth history—have exhibited an exceedingly long-term lack of discernable change consistent with their asexual reproduction (6).
Given these observations, it might be tempting to interpret such sulfur-cycling communities as evidencing the “negative” null hypothesis of Darwinian evolution—if there is no change in the physical biological environment of a well-adapted ecosystem, there should be no speciation, no evolution of the form, function, or metabolic requirements of its biotic components—a confirmation of Darwin’s theory that seems likely to be provided only by ecosystems fossilized in an environment that has remained essentially unaltered over many hundreds of millions of years.
Although logically required, this aspect of evolutionary theory has yet to be established.
In my last class we discussed the view that natural selection is the only mechanism of evolution (false). We then discussed the view that evolution only occurs when the environment changes (false). Finally, we tried to imagine how any species could become so perfectly adapted to it's current environment that further increases in fitness are impossible (silly).
Along comes a new paper by William Schopf whose earlier claim to fame was the discovery of 3.5 billion year old fossils. A claim that has been discredited. The "fossils" weren't fossils [Did Life Arise 3.5 Billion Years Ago?]. The latest study was funded by the NASA Astrobiology Institute.
I can't read the paper right now because I don't have access but here's the summary from PNAS.
Americans have changed their flag many times1 but Canada did it only once, on Feb. 15, 1965 [Flag of Canada]. Today is the 50th anniversary.
Even Goggle celebrates.
1. The last time was in 1960.
Vincent Joseph Torley (vjtorley) didn't like my recent post where I said there was no evidence for the existence of god(s) [Evidence for the existence of god(s)]. The reason this is important is because I define science as a way of knowing that, among other things, relies on evidence. If you believe in something without supporting evidence then that conflicts with science as a way of knowing. There may be other ways of knowing that do not rely on, or conflict with, evidence but you first have to convince me that the knowledge produced by this other method is actually true knowledge.
Here's what I said in that post ...
I am always on the lookout for evidence that some sort of god actually exists. The reason I'm an atheist is because I've never seen any evidence that's the least bit convincing. I keep asking for evidence but nobody ever supplies any.
Vincent Torley ctiiticizes me for not making a clear distinction between "evidence" and "convincing evidence" and he is correct [see No evidence for God’s existence, you say? A response to Larry Moran]. When I say there's no evidence for the existence of god(s) I mean that there is no "evidence" that stands up to close scrutiny. That's not quite the same thing as saying that there's no "evidence" that others might believe or no potential facts that are presented as possible evidence.
It's an important distinction to keep in mind but It think it quite clear that when I say there's no evidence for the existence of god(s) I mean that there's no valid evidence. That brings up the question of what defines "valid evidence." The short answer is "I don't know" but I know it when I see it.
Let's look at one of Vincent Torley's claims that there's evidence for god(s); namely, the evidence of miracles. Note that he accepts the process of science. In other words, he is willing to defend his belief that god(s) exist by pointing to "valid evidence" that his belief is correct. What that means is that we discuss his claim using the ground rules of science according to my view of what science is.1
Professor Moran will want to see good evidence of miracles, so I’ll confine myself to one case: the 17th century Italian saint, Joseph of Cupertino, who was seen levitating well above the ground and even flying for some distance through the air, on literally thousands of occasions, by believers and skeptics alike. The saint was the phenomenon of the 17th century. Those who are curious might like to have a look at his biography by D. Bernini (Vita Del Giuseppe da Copertino, 1752, Roma: Ludovico Tinassi and Girolamo Mainardi). The philosopher David Hume, who was notoriously skeptical of miracle claims, never even mentions St. Joseph of Cupertino in his writings. Funny, that.
The evidence for St. Joseph’s flights is handily summarized in an article, The flying saint (The Messenger of Saint Anthony, January 2003), by Renzo Allegri.
If I were to accept the claim advanced by Vincent Torley then this would, indeed, constitute evidence that something very weird happened back in 1630. But I reject the claim. I simply don't believe that people actually witnessed Joseph of Cupertino flying through the air. It's not a fact. It's not evidence.
This is a case where an extraordinary claim requires extraordinary evidence. You can't just rely on what people say they saw because if that's all you need then there must be fairies at the bottom of the garden. And UFO abductions would be real.
Read Vincent Torley's other claims of "evidence" for the existence of god(s). Some of them are quite interesting but most of them are just wishful thinking. Take "fine tuning" for example. If the universe is really "fine tuned" for the existence of life—and that is disputed by many scientists—then why does that constitute evidence of gods? We could not possibly find ourselves in any universe that was not compatible with the existence of life. If this universe arose entirely by accident then we would still be here discussing the meaning of evidence.
Fine tuning is not evidence that gods exist. The best that could be said is that if you believe in gods then you can construct stories about supernatural beings who made the universe with the goal of producing life on one small insignificant planet near the edge of an otherwise unremarkable galaxy. If you don't believe in gods then it all looks pretty haphazard.
1. If you believe that science cannot address any claim that involves the supernatural then, presumably, you will have to dispute Vincent Torley's claim using some other way of knowing. I don't know what that is. Perhaps one of you can describe it for me?
For those or you who are still interested in the debate over the nature of science and how it played out in Kitzmiller v. Dover Area School District back in 2005, I present to you ....
A Reading List
Science at the Bar—Cause for Concern by Larry Laudan
Many of you have heard stories about Micheal Behe's testimony in Kitzmiller v. Dover Area School District. Some of you have even made fun of him for saying that astrology is science.
The transcript of Behe's testimony is here. The important bits are when the lawyer for the plaintiffs is discussing the definition of "theory."
Q But the way you are using it is synonymous with the definition of hypothesis?
A No, I would disagree. It can be used to cover hypotheses, but it can also include ideas that are in fact well substantiated and so on. So while it does include ideas that are synonymous or in fact are hypotheses, it also includes stronger senses of that term.
Q And using your definition, intelligent design is a scientific theory, correct?
A Yes.
Q Under that same definition astrology is a scientific theory under your definition, correct?
A Under my definition, a scientific theory is a proposed explanation which focuses or points to physical, observable data and logical inferences. There are many things throughout the history of science which we now think to be incorrect which nonetheless would fit that -- which would fit that definition. Yes, astrology is in fact one, and so is the ether theory of the propagation of light, and many other -- many other theories as well.
Q The ether theory of light has been discarded, correct?
A That is correct.
Q But you are clear, under your definition, the definition that sweeps in intelligent design, astrology is also a scientific theory, correct?
A Yes, that's correct. And let me explain under my definition of the word "theory," it is -- a sense of the word "theory" does not include the theory being true, it means a proposition based on physical evidence to explain some facts by logical inferences. There have been many theories throughout the history of science which looked good at the time which further progress has shown to be incorrect. Nonetheless, we can't go back and say that because they were incorrect they were not theories. So many many things that we now realized to be incorrect, incorrect theories, are nonetheless theories.
Q Has there ever been a time when astrology has been accepted as a correct or valid scientific theory, Professor Behe?
A Well, I am not a historian of science. And certainly nobody -- well, not nobody, but certainly the educated community has not accepted astrology as a science for a long long time. But if you go back, you know, Middle Ages and before that, when people were struggling to describe the natural world, some people might indeed think that it is not a priori -- a priori ruled out that what we -- that motions in the earth could affect things on the earth, or motions in the sky could affect things on the earth.
I've seen lots of people mock Michael Behe for saying that astrology is science but I doubt they have read the actual transcript. Even if they have, I doubt that they appreciate the difficulties in deciding whether something is science or not.
Bad science doesn't always become pseudoscience. Most bad hypotheses just die a quiet death when they are discredited. The transition to pseudoscience only happens when the proponents refuse to give up and insist that their theory is still valid science.
The point is, bad science and pseudoscience are science or at least they were accepted as possible scientific explanations until they were discredited. If they weren't within the realm of science then they could never have been falsified by science.
If you think you know how to define science in a way that eliminates all those ideas that you don't like then read: Is Astrology a Science?
You might not be so inclined to make fun of Michael Behe after that.
[Reposted from 2008.]
Charles Robert Darwin was born on this day in 1809. Darwin was the greatest scientist who ever lived.
In honor of his birthday, and given that this is a year of politics in America, I thought it would be fun to post something about Darwin's interactions with politicians. The historical account is from Janet Browne's excellent biography (Brown 2002).
William Gladstone (photo below) was an orthodox Christian. He was not a fan of evolution. In March 1877 Gladstone was leader of the Liberal party and a former Prime Minister of the most powerful country in the world. He was spending the weekend with John Lunnock—a well-known liberal—and a few other friends, including Thomas Huxley.
They decided to walk over to Darwin's House in Downe. This was 18 years after the publication of Origins and Darwin was a famous guy. The guests were cordially received by Darwin and his wife Emma. Darwin and Emma were life-long liberals and they were honored by Gladstone's visit. A few days later, Darwin wrote a note to his friend saying,
Our quiet, however, was broken a couple of days ago by Gladstone calling here.—I never saw him before & was much pleased with him: I expected a stern, overwhelming sort of man, but found him as soft & smooth as butter, & very pleasant. He asked me whether I thought that the United States would hereafter play a much greater part in the history of the world than Europe. I said that I thought it would, but why he asked me, I cannot conceive & I said that he ought to be able to form a far better opinion,—but what that was he did not at all let out.
A few years later Gladstone sent Darwin one of his essays on Homer. Darwin gratefully acknowledged the gesture.
In 1881, when Gladstone was Prime Minister again, Darwin and some of his friends petitioned Gladstone to award a pension to Alfred Russel Wallace, who was in dire financial straits at the time. Gladstone granted the request. Two months later Gladstone offered Darwin a position as trustee of the British Museum but Darwin declined. (Remember, Gladstone did not agree with Darwin about evolution, or religion.)
When Darwin died, Gladstone was instrumental in arranging for him to be buried in Westminster Abbey. The funeral was held on April 26, 1882. William Gladstone was too busy to attend. He went to a dinner at Windsor.
Brown, J. (2002) Charles Darwin: The Power of Place (Vol. II). Alfred A. Knopf, New York (USA)
My friend, Robert Day, (Canadian Cynic) was subjected to a vicious and protracted serial defamation by Patrick Ross. Wanna know what happened?
Read: Patrick Ross, and the end of a very long road..
We're discussing the nature of science by attempting to answer the question, "What is science?"
The example I've chosen is the debate over intelligent design (ID) and whether it is science or not. Many people believe that the question was settled by Judge Jones in Kitzmiller v. Dover Area School District: Decision of the Court. His answer was "no," intelligent design is not science.
In my first post I went over part of his decision in order to show that the issue is a lot more complicated than most people think [What did Judge Jones say in 2005? (Part I)]. It turns out that there are many ways to define science and Judge Jones picked one in order to prove that ID is not science. But there are other definitions of science where ID would qualify as science.
A lot of my ideas come from a recent book called Philosophy of Pseudoscience: Reconsidering the Demarcation Problem. Much of that book is based on philosopher Larry Laudan's view of the demarcation problem. Here's a relevant passage (p. 111)...
