The University of Toronto publicity department is making a big deal of Rachel Harding. She's a post-doc in the Structural Genomics Consortium (SGC). She works on Huntington's disease.
Faculty of Medicine researcher Rachel Harding will be the first known biomedical researcher to welcome the world to review her lab notes in real time. The post-doctoral fellow with U of T’s Structural Genomics Consortium (SGC) is also explaining her findings to the general public through her blog. She hopes her open approach will accelerate research into Huntington’s disease.
“This should drive the process faster than working alone,” Harding says. “By sharing my notes, I hope that other scientists will critique my work, collaborate and share data in the early stages of research.” Her research at SGC is funded by CHDI Foundation, a non-profit drug-development organization exclusively dedicated to Huntington’s disease. Both organizations aim to accelerate research by making it open and collaborative.
Her approach is intended to leverage the experience of a community of scientists. Individual researchers often still work in relative isolation and then publish only their positive discoveries, usually years after the experiments were actually done. Thus, scientists often pursue similar ideas in parallel and miss many opportunities to learn from each other’s mistakes.
She has started by publishing raw data and play-by-play details of her first effort on the CERN open digital repository Zenodo. She also posts regular updates on her blog Lab Scribbles, where she includes an experimental summary written in lay terms.
It's been over 35 years since I first starting thinking and talking about electronic (computerized) lab notes1 and it's been over twenty years since I first heard discussions about putting them online. I seriously doubt that Rachel Harding is the first biomedical researcher to put lab notes on the web. I'm also very skeptical about her keeping up the practice for very long.
Not only is it boring and tedious to write your lab notes in a word processing program but it's kinda embarrassing to post everything you do in the lab. At least it would have been for me. I made lots of mistakes and there are lots of R-rated words and phrases in my notes.
Let's keep an eye on this experiments to see how it goes. So far there are four items on the Zenodo website. The first is a Word document containing a few brief notes from Jan. 6, 7, 9, 11 and 25. There are brief notes posted on Feb. 6 and two on Feb. 11. I hope this isn't the extent of her lab notes.
The blog is Lab Scribbles. There are a few posts. It's interesting but I'm not sure anyone is going to read it even if you're interested in Huntington's.
Has anyone else experimented with open lab notes?
1. I still have a few floppy disks with those attempts from about 1981. Unfortunately, I don't have a machine that can read them.
The first drafts of the human genome sequence were published in 2001. There was still work to do on "finishing" the sequence but a lot of the International Human Genome Project (IHGP) team shifted to work on the mouse genome. The FANTOM Consortium and the RIKEN Genome Exploration Groups (I and II) published an analysis of mouse transcripts in December 2002.
Okazaki, Y., Furuno, M., Kasukawa, T., Adachi, J., Bono, H., Kondo, S., Nikaido, I., Osato, N., Saito, R., Suzuki, H. et al. (2002) Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature, 420:563-573. [doi: 10.1038/nature01266]
Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 ‘transcriptional units’, contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense–antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.
Postgenomics is a compendium of twelve scholarly articles by philosophers and sociologists who write about the implication of the human genome sequence and subsequent work on interpreting the results. The volume is edited by Sarah Richardson, a professor in Social Sciences (History of Science) at Harvard University (Boston, Massachusetts, USA), and by Hallam Stevens, a professor of History at Nanyang Technology University in Singapore (Singapore).
The first essay is by Stevens and Richardson and it outlines the goal of the book.
One of the biggest problems with the Intelligent Design Creationist movement is their attempt to corral all creationist under the same big tent. This leads to a situation where Young Earth Creationists are afforded the same level of respect as those who accept common descent and an ancient Earth.
It means that dissent within the ID community is strongly suppressed in order to maintain the illusion that they all agree on the basics (i.e. goddidit). This leads to ridiculous situations where Young Earth Creationists defend Stephen Meyer's attack on the Cambrian explosion in Darwin's Doubt when they don't even believe that the Earth is 500 million years old!
There's no consistency in the arguments from ID proponents so it's almost impossible to have a serious discussion of the science behind their claims. I've criticized ID proponents for not applying critical thinking to their own movement. They almost never dispute each other's ideas for fear that it would weaken their movement.
That fear is justified, but what they fail to realize is that the movement doesn't deserve any respect at all if they don't apply the same standards to their own views that they demand of others.
To their credit, a few members of the movement have started to change this long-standing attempt to silence dissent within the movement. I think they realize that the respect they crave will only come from kicking a few people out of the tent.
One of those people is Vincent Torley. He has posted an excellent discussion of Denton's structuralist views on Uncommon Descent: Denton vs. Moran on structuralism. I don't agree with everything Torley says but I congratulate him for his courage in thinking critically about Michael Denton's position.
It will be interesting to see if the Intelligent Design Creationist movement can deal with critical thinking. I'm watching the comments on the blog post.
Here's a video where Michael Denton describes his view of biology. The main point is that he cannot think of a way for evolution to produce the "hierarchy of nature." Therefore goddidit there must be some other explanation.
Darwinism, honestly regarded, should lead you to expect not an ordered, increasingly inclusive hierarchy of life but more like a disordered...smear of diversity. Such expectations are frustrated by reality. As biologist Michael Denton explains, life presents itself as a tiered formation marked by novelties or homologs. These taxa-defining novelties, such as the pentadactyl limb, are not lead up to by a series of forms increasingly like the final version.
That's strike one. Worse for Darwinism, it's typically the case that there is no way even to imagine how the novelty could be lead up to in such a manner. Strike two. Watch and enjoy.
Has a scientific explaination of the universe replaced the need for God as cause of its origins? Could life on our planet exist apart from divine intervention? Is there evidence for a designer?
On March 19th, three big thinkers, well-known in their various fields, will be together for the first time, on the stage at the University of Toronto’s Convocation Hall discussing God, science and the universe:
Lawrence M. Krauss World-renowned Theoretical Physicist
Stephen C. Meyer Cambridge educated author and intelligent design advocate
Denis O. Lamoureux Science and Religion professor from the University of Alberta
Questions like these will be posed to the panel:
How did the universe originate?
Does God play any role in the cosmos?
What is the relationship between science and religion?
You are invited to live-stream this event via YouTube at your venue free of charge. Once you register as an event host, Wycliffe College and our partners will be happy to provide you with promotional and follow-up material to help make your event a success.
As evidenced by our sponsors, this is an opportunity that spans the diverse interests and questions of the scientist, the scholar, the layperson, the young and the old, and the Atheist, Agnostic and Christian. Our goal is to be a catalyst in starting conversations around our country on issues of faith and their intersection with broader society.
Join thousands in Toronto and around the globe to take part in this rare and exciting opportunity.
Most of you are familiar with the long-term evolution experiment (LTEE) run by Richard Lenski. One of the cultures in that experiment evolved the ability to use citrate as a carbon source. Normally, E. coli cannot use this carbon source under aerobic conditions but the new strain not only utilizes citrate but can grow in cultures where citrate is the only source of organic carbon.
A large statue of Charles Darwin was installed in the main foyer of the London's Natural History Museum in 1885—just a few years after Darwin's death. It was removed in 1927 and replaced by a statue of Richard Owen who was no fan of Darwin.
The museum came to its senses in 2009 and put the statue back in it's original position. (It had been in the cafeteria in the basement.) Read the story at: Moving Darwin.
Owen was the man who founded the museum and he was also known for his support of structuralism—the idea that basic body plans cannot be easily explained by evolution. Structuralism is the new buzzword among Intelligent Design Creationists. They don't understand the concept but they're certain it refutes evolution and supports goddidit.
Watch Paul Nelson combine his lack of knowledge of evolution and evolutionary theory with misinformation (i.e. lies) and a little bit of false developmental biology then stir the pot with a large dose of god-of-the-gaps to produce a smooth argument that refutes evolution.
There's lots of other stuff going on in this talk. I was especially amused by the discussion of methodological naturalism at the end. Paul Nelson argues that science is blind to all the evidence of a creator because the "rule" of science is that it can't even consider that evidence.
I'll say one thing about this talk: it's very clever. It would take a book to show that Paul Nelson is wrong about everything and the explanations would be far too complicated for the average creationist. For them, it's easier to believe that Paul Nelson is telling them the truth and evolutionary biologists are too stupid to understand their own discipline.
Otangelo Grasso has posted a transcript of the talk. Thank-you Otangelo.
The draft sequences of the human genome were published fifteen years ago. The International Human Genome Project (IGHP) published its draft sequence in Nature on Feb. 15, 2001 (Lander et al., 2001) and Celera Genomics published its draft sequence in Science on Feb. 16, 2001 (Venter et al., 2001).1
For me the timing was perfect since I was scheduled to give a Journal Club talk on March 16th and you could hardly ask for a better topic.
Antonin Gregory Scalia (March 11, 1936 – February 13, 2016), justice of the Supreme Court of the United States, died a few days ago. This creates a crisis in American politics because they have a strange set of Constitutional requirements guaranteed to maximize the probability of crises every time they need a new Supreme Court justice.
Scalia's death reminded me of the dissenting opinion in EDWARDS V. AGUILLARD (June 19, 1987). This was the case that invalidated Louisiana's "Balanced Treatment for Creation-Science and Evolution-Science Act." Stephen Jay Gould was puzzled by the dissenting opinion so he wrote a wonderful essay to explain Justice Scalia's Misunderstanding.
It's worth reading the entire essay but here's the conclusion,
Following this theme, Scalia presents his most confused statement in the written dissent:
Creation science, its proponents insist, no more must explain whence life came than evolution must explain whence came the inanimate materials from which it says life evolved. But even if that were not so, to posit a past creator is not to posit the eternal and personal God who is the object of religious veneration.
True indeed; one might be a creationist in some vernacular sense by maintaining a highly abstract and impersonal view of the creator. But Aristotle's unmoved mover is no more part of science than the Lord of Genesis. Science does not deal with questions of ultimate origins. We would object just as strongly if the Aristotelophiles of Delaware forced a law through the state legislature requiring that creation of each species ex nihilo by an unmoved mover be presented every time evolution is discussed in class. The difference is only historical circumstance, not the logic of argument The unmoved mover doesn't pack much political punch; fundamentalism ranks among our most potent irrationalisms.
Consider also, indeed especially, Scalia's false concept of science. He equates creation and evolution because creationists can't explain life's beginning, while evolutionists can't resolve the ultimate origin of the inorganic components that later aggregated to life. But this inability is the very heart of creationist logic and the central reason why their doctrine is not science, while science's inability to specify the ultimate origin of matter is irrelevant because we are not trying to do any such thing. We know that we can't, and we do not even consider such a question as part of science.
We understand Hutton's wisdom. We do not search for unattainable ultimates.
We define evolution, using Darwin's phrase, as "descent with modification" from prior living things. Our documentation of life's evolutionary tree records one of science's greatest triumphs, a profoundly liberating discovery on the oldest maxim that truth can make us free. We have made this discovery by recognizing what can be answered and what must be left alone. If Justice Scalia heeded our definitions and our practices, he would understand why creationism cannot qualify as science. He would also, by the way, sense the excitement of evolution and its evidence; no person of substance could be unmoved by something so interesting. Only Aristotle's creator may be so impassive.
Who was Saint Valentine? Nobody really knows very much about the Saints Valentine (there were about a dozen of them). The whole idea of romantic Valentine's day seems to have been invented by Geoffrey Chaucer1 sometime around 1380.
It seems like people in England just wanted to enjoy a bit of debauchery fun on February 14th so they connected their frolics with a Roman Catholic saint in order to get the permission of the church! Pretty clever, eh?
Readers of this blog will know that I'm a fan of Evolution by Accident. I don't think that the history of life can be explained in strict Darwinian terms (i.e. natural selection) and I think that modern evolutionary theory includes Neutral Theory and a major role for random genetic drift.
This is the view of many modern evolutionary biologists. Their work and views have been reported frequently on Sandwalk over the past ten years but you can find it in all the evolutionary biology textbooks. I'm just the messenger here. It's evolutionary biologists who have made the case for non-adaptive evolution beginning long before The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme.
This is another post about the stupidity of Intelligent Design Creationists. Stop reading if you don't need any more convincing.
Today is Darwin Day. It's the anniversary of the birth of Charles Darwin (Feb. 12, 1809 - April 19, 1882).
This is not a happy day for the Discovery Institute so they've put up a series of posts on Evolution News & Views (sic) to discredit Darwin and "Darwinism."
To understand the core weakness of the Darwinian worldview, it is important to understand what Darwinian natural selection requires. The process will work its magic, building up functional structures in organisms, only when two very strict conditions are met: First, the structure must be adaptive—that is, helpful to the organism in flourishing in its environment—and second, there must be a continuum of structures, functional all along the way, leading from an ancestor species to the descendent.
That is, the thing we are trying to explain must in some way help the creature survive, and between the creature and the creature's ancestor there must be a gradual change, each step of which is stable and enhances fitness, or success in reproduction.
Strictly speaking, that's a reasonable explanation of Darwinism as most evolutionary biologists understand it. But here's the problem. There aren't very many evolutionary biologists who are strict Darwinists these days even though there are many who tilt strongly in that direction.
Intelligent Design Creationists are promoting a structuralist view of evolution [What is structuralism?]. The idea is that the history of life as we know it was largely preordained by the initial laws of physics and chemistry. According to this view, once life got under way it was inevitable that it would eventually evolve the way it did resulting in humans or something that closely resembles humans.
Structuralism is based on the idea of intrinsic forms that severely limit evolutionary pathways. These forms are constrained, and defined, by the physics of matter and energy. Some creationists like this idea because they believe that god created the universe and fine-tuned it for life. According to their faith, once the original laws of physics and chemistry were set up it was just a matter of time before humans evolved. These creationists can make their belief in a creator god compatible with evolution as they see it.
(Let's not forget that there are many structuralists who are legitimate scientists and some of them are atheists. Structuralism is not a creationist invention.)
The conflict between structuralists and others is brought into focus by Stephen Jay Gould writing in Wonderful Life.
The blog "Conceptual Revolutions in Science" only publishes "evidence-based, paradigm-shifting scientific news" according to their home page.
The man behind the website is Adam B. Dorfman (@DorfmanAdam). He has an MBA from my university and he currently works at a software company. Here's how he describes himself on the website.
Some of you are aware of recent attacks on Richard Dawkins. This video by Brian Dalton (Mr. Deity)1 is directed at certain people who have led the attacks. Some of them are my friends but I'm having second thoughts. They should pay close attention.
I disagree with several scientific ideas that Richard Dawkins has promoted and we have discussed these disagreements in person and on the internet. I've always found him to be polite and respectful.
Michael Denton and the Discovery Institute are promoting his new book, Evolution: Still a Theory in Crisis. I haven't yet read the book. I ordered from Amazon.ca and I won't get it until March.
The essence of the fine-tuning argument is that the basic laws of physics and chemistry are so precise that even slight changes would result in a universe where life is impossible. The focus is usually on the fundamental constants such as the speed of light and the charge on an electron. I don't know enough about physics to evaluate the argument that these are fine-tuned so I have to rely on physicists to inform me.
All available evidence suggests that we are quite likely the only advanced life form in the Milky Way galaxy. Maybe our planet harbors the only life in the entire universe.
Matthew Cobb wasn't happy with the way Denis Alexander reviewed Jerry Coyne's book. Recall that Denis Alexander is a biochemist at Cambridge University (UK) and we had a little debate a week or so ago [Is there a conflict between science and religion?]. His position is that there's no conflict between science and religion because a person who believes in god can always make their views conform to the discoveries of science. I didn't accept his premise—that gods exist—so we had a discussion about whether there's any evidence to support his belief in god.
If you believe in such a being then that conflicts with science as a way of knowing because you are believing in something without reliable evidence to support your belief. Scientists shouldn't do that and neither should any others who practice the scientific way of knowing. Denis Alexander thinks there are other, equally valid, ways of knowing but he wasn't able to offer any evidence that those other ways produce true knowledge.
Matthew Cob wrote a letter to the editor in which he asked, "I wonder if Dr Alexander, or indeed any reader, could provide an example of knowledge gained through theology, and above all tell us how they know that knowledge is true?" [see Matthew Cobb battles with the faithful over my book].
Jerry Coyne discovered a Quiz on DNA. He calls is a so-so quiz on DNA. He says that one question is really, really, dumb. I disagree, I think there are several dumb questions.
I tried it and got a score of 19/19 in just under four minutes. This is misleading since you have to get every question right before continuing on to the next question. I had to anticipate what the authors wanted in order to proceed.
Try the quiz yourself before reading any further. There are spoilers below!
The Intelligent Design Creationists are promoting Michael Denton's new book Evolution: Still a Theory in Crisis. The new buzzword is "structuralism" and it's guaranteed to impress the creationist crowd because nobody understands what it means but it sounds very "sciency" and philosophical. Also, it's an attack on "Darwinism" and anything that refutes evolution has to be good.
You can watch Michael Denton explain structuralism ... it only takes a few minutes of your time.
You are probably wondering why "Darwinism" persists after the creationists have thoroughly demonstrated that it is a failed theory. Lucky for you, the most intelligent and intellectual of all Intelligent Design Creationists, David Berlinski and Michael Denton, have gotten together to explain it in a short (15 mins) podcast.
If the most brilliant Darwin critics, like David Berlinski and Michael Denton, are right, how then does Darwinism hang on? How does a failed theory maintain its grip on our science and on our culture? Why is there a sense of stalemate? On ID the Future, we posed these questions to Dr. Berlinski and Dr. Denton.
If you are interested in the conflict between Intelligent Design and science you owe it to yourself to see/hear the best they've got on their side.
You can always dream. While the evolutionist side in the Darwin debate is long on rhetoric and insults, serious debate or dialogue is woefully rare. But imagine you had the opportunity to sit down with a thoughtful, honest, well-informed Darwinist and pose one question or challenge. What would it be?
I had the opportunity to pose that question to two of the most brilliant minds in the intelligent design community -- Michael Denton and David Berlinski. Take a well-spent 15 minutes and listen to their answers -- focusing respectively on the insect body plan and the enigma of whale evolution -- recorded as an episode of ID the Future.
Berlinski wants a detailed mathematical estimate of the number of mutations required to go from a land animal to a whale. Denton wants details on the formation of insect body plans.
It's important to note that these are questions about the history of life. You could easily answer "I don't know" to both questions and it would not affect our understanding of evolution and common descent one iota. The answers have nothing to do with "Darwinism" per se and nothing to do with evolutionary theory (which is not Darwinism).
Listen to the very best minds in the Intelligent Design Creationist community ... and weep for them. This is all they've got.
Richard Dawkins published The Selfish Gene 40 years ago and Matt Ridley notes the anniversary in a Nature article published today (Jan. 28, 2016): In retrospect: The selfish gene.
I don't remember when I first read it—probably the following year when the paperback version came out. I found it quite interesting but I was a bit put off by the emphasis on adaptation (taken from George Williams) and the idea of inclusive fitness (from W.D. Hamilton). I also didn't much like the distinction between vehicles and replicators and the idea that it was the gene, not the individual, that was the unit of selection ("selection" not "evolution").
It is finally time to return to the problem with which we started, to the tension between individual organism and gene as rival candidates for the central role in natural selection...One way of sorting this whole matter out is to use the terms ‘replicator’ and ‘vehicle’. The fundamental units of natural selection, the basic things that survive or fail to survive, that form lineages of identical copies with occasional random mutations, are called replicators. DNA molecules are replicators. They generally, for reasons that we shall come to, gang together into large communal survival machines or ‘vehicles’.
Currently there are two distinct views on the origin of life. The majority of scientists think that life arose in a prebiotic soup of complex organic molecules. Most of them think this "warm little pond" was the ocean (!) and most of them have bought into the stories about asteroids and comets delivering complex organic molecules to create a soup of amino acids and sugars. Presumably, all the earliest forms of life had to do was to join together the amino acids to make proteins and hook up the nucleotides to make RNA. The energy for these reactions was derived from breaking down all the glucose in the sweet ocean.
James McGrath is a professor of religion at Butler University in Indianapolis, Indiana, USA.
He is one of those "sophisticated theologians" who dismiss modern atheists because we haven't spent years studying theology and because we haven't experienced the true existential angst of Jean-Paul Sartre. As a group, they hold to the position that the "New Atheists" are amateurs in the study of religion and their arguments can be easily dismissed.
Back in 2010, Richard Dawkins was answering questions on Reddit and one of the questions was "Out of all the evidence used to support the theory of evolution, what would you say is the strongest, most irrefutable single piece of evidence in support of the theory."
There are several ways to answer this question. Personally, I would take a minute to explain the difference between the "theory of evolution" and the history of life. I would point out that evolutionary theory includes things like Darwin's natural selection and there is overwhelming evidence proving that natural selection exists and operates today. The entire field of population genetics, which included other mechanisms of evolution such as random genetic drift, is massively supported by thousands of published papers in the scientific literature. There is absolutely no doubt at all that the current basic tenets of evolutionary theory are correct.
Confirmation bias is one of the major logical fallacies. When philosopher Chris DiCarlo and I were teaching a course on critical thinking we used to spend quite a bit of time on it because it's a very common trap. We are all guilty, from time to time, of focusing on just the evidence that confirms our belief and ignoring all the evidence that refutes it.
Some examples of confirmation bias are a bit more complicated than others and people typically mix together several different fallacious forms of argument. Here's an example from Denis Alexander's book Creation or Evolution (p. 213) that combines begging the question and confirmation bias.
Denis Alexander is a biochemist at the University of Cambridge (UK). I thought I'd share one of the stories in his book.
At the church I attend in Cambridge we baptised an undergraduate in the natural sciences who had come to a personal, saving faith in Christ from a completely atheistic background. As is usual in our church, just before being baptised she explained publicly to the whole congregation how she had become a Christian, telling us she had become convinced there must be a God while sitting through a standard biochemistry lecture, hearing the amazing story of how two meters (about six feet) of DNA are packaged into a single cell. Of course the lecturer was not talking in religious terms at all, but she described to us how the beauty of that engineering feat overwhelmed her as she listened, giving her the deep intuition there must be a God, so leading her onward in he personal pilgrimage to put her trust in this creator God through Christ. Truly natural theology at work!
That got me thinking. I've been describing chromatin and packing in my textbooks since the first version in 1987. There must have been several hundred thousand students who have read my descriptions since then.
The post is from Dec. 1, 2015—that's only one month ago so she should be aware of all the facts concerning junk DNA.
If you are going to write about a subject in your area of expertise then it's reasonable to make yourself informed, especially if you know that the subject is controversial. For some strange reason, this common sense approach seems to be ignored when discussing genomes, evolution, and junk DNA. I don't know why some researchers think they know enough about a subject when all they've done (apparently) is read a few popular press reports.
Let's look at what Bryony Graham (@byrony_g) writes to see whether she is behaving like a proper scientist should behave when writing for the general public. It's worth noting that she was on the shortlist for the 2011 Max Perutz Science Writing Award so somebody must think she's a good science writer.
The sequence of the human genome was announced on June 26, 2000 although the actual sequence wasn't published until a year later. There were two sequences. One was the product of the International Human Genome Project led by Francis Collins who said,
"It is humbling for me and awe-inspiring to realize that we have caught the first glimpse of our own instruction book, previously known only to God."
The sequence was a composite of a number of individuals.
The second sequence was from Celera Genomics, led by Craig Venter. It was mostly his genome, making him the second being to know his own instruction book ... right after God.
It took another seven years to finish and publish the complete sequence of all of Craig Venter's chromosomes. The paper was published in PLoS Biology (Levy et al., 2007) and highlighted in a Nature News article: All about Craig: the first 'full' genome sequence.
What's unique about this genome sequence—other than the fact that it's God's Craig Venter's—is that all 46 chromosomes were sequenced. In other words, enough data was generated to put together separate sequences of each pair of chromosomes. That produces some interesting data.
There were 4.1 million differences between homologous chromosomes (22 autosomes). 78% of these events were single nucleotide polymorphisms (SNPs). The rest were indels (insertions and deletions) and these accounted for 0.9 million nucleotides. Thus, indels made up 74% of the total number of variant nucleotide sequence.
In addition, there were 62 copy number variants (duplication) accounting for an additional 10Mb of variation between haploid sets of chromosomes. The total number of nucleotide differences is 13.9Mb when you add up all the indels, SNPs, and duplications. The two haploid genomes differ by about 0.5% by this calculation (total amount sequenced was 2,895Mb).
When the two copies of all annotated genes were compared, it turned out that 44% were heterozygous—the two copies were not identical.
Craig Venter's genome sequence differs from the composite human reference genome at 4,118,889 positions. Most of these were already known as variants in the human population but 31% were new variants (in 2007).
Venter has written about his genome sequence in A Life Decoded. He has variants in his APOE gene sequence that are associated with Alzheimer's and cardiovascular diseases. He has variants in his SORL1 that also make him at risk for Alzheimer's according to 2007 data. Just about everyone who gets their genomes sequenced will find variants that put them at greater risk for some genetic disease.
Massimo Pigliucci is an atheist who thinks that science and religion are compatible because they rule in different domains. He takes a very narrow view of "science"— one that excludes the work of historians and philosophers who are presumably using some other way of knowing. (He doesn't tell us what that is.)
I prefer the broad view of science as a way of knowing that relies on evidence, rational thinking, and healthy skepticism. This broad view of science is not universal—but it's not uncommon. In fact, Alan Sokel has defended this view of Massimo Pigiucci's own blog: [What is science and why should we care? — Part III]. According to this view, any attempt to gain knowledge should employ the scientific worldview. Historian and philosophers should follow this path if they hope to be successful. Pigliucci should know that there are different definitions and any discussion of the compatibility of science and religion must take these differences into account.
We know quite a lot about the origin of new genes (Carvunis et al., 2012; Kaessman, 2010; Long et al., 2003; Long et al., 2013; Näsvall et al., 2012); Neme and Tautz, 2013; Schlötterer, 2015; Tautz and Domazet-Lošo (2011); Wu et al., 2011). Most of them are derived from gene duplication events and subsequent divergence. A smaller number are formed de novo from sequences that were not part of a gene in the ancestral species.
In spite of what you might have read in the popular literature, there are not a large number of newly formed genes in most species. Genes that appear to be unique to a single species are called "orphan" genes. When a genome is first sequenced there will always be a large number of potential orphan genes because the gene prediction software tilts toward false positives in order to minimize false negatives. Further investigation and annotation reduces the number of potential genes.
Thanks for reading the commentary on my university’s communication page, hastily written for brevity and digestibility by me and our science communication officer, Lawrence Goodman. I was originally hoping the piece could focus on my latest research, but it turned into this sort of general Q&A chat. The commentary was written rather quickly and meant for a general audience perusing Brandeis research, so it is obviously not a peer-reviewed scientific publication.
I am well aware of both your reputations as fiery critics and experts of evolutionary biology, and you have somewhat of a following on the internet. Some of your earlier blog posts have been entertaining and even on point regarding how big projects like ENCODE have over-hyped the functional proportions of our genomes. So, it does NOT surprise me one bit that I would become your latest vitriolic target in your posts here, and here.
Could I learn more from you two about evolutionary biology theory? Indeed, I could. Can we revise our Q&A commentary to be more scientifically accurate while still being digestible to a general audience? Perhaps, if we have the time and I survive my tenure review, we may do so and take your input into consideration. Why respond and risk another snarky post from you guys? I could care less about your trivial blog critiques when I’ve received plenty of grants and paper rejections that cut much deeper into my existence as a young academic struggling to survive when the academic track has never been more challenging (<10% grant success rates at NIH, NSF, CIHR, etc).
I’m responding to ask that both of you reflect on the message your posts are sending to students and postdocs. As a young scientist, having a chat with my university PR rep, I have to now think twice about two senior tenured professors slamming my scientific credibility on your internet soapbox without a single direct email to me. How passive-aggressive!
Your message is saying that Academic science even less inviting to young scientists as it is, with faculty positions and grants falling way short of demand, and the tough sacrifices every young scientist is already making for the craft that we love. If we condone this type of sniping behavior, why would any young scientist want to learn and discuss with the older scientists of your generation?
A direct email from you to me expressing your scientific concerns of our commentary would have been a better way to go. I am willing to stand corrected. Your blog posts, however, are disappointing and appear petty to me. Let’s all set a better example here for our trainees.
If you wish to post this response verbatim on your blogs, go ahead, since I had thought of posting this response on your blog’s comments section. But to follow my own advice, I’ll try a direct email to you first. And if I don’t hear back from you, I may then ask my friend Bjorn to help me post this on his blog.
This time it's Assistant Professor of Biology Nelson Lau. He studies Piwi proteins and PiRNAs.
Lau was interviewed by Lawrence Goodman, a science communication officer at Brandeis University: DNA dumpster diving. The subject is junk DNA and you will be astonished at how ignorant Nelson Lau is about a subject that's supposed to be important in his work.
How does this happen? Aren't scientists supposed to be up-to-date on the scientific literature before they pass themselves off as experts? How can an Assistant Professor make such blatantly false and misleading statements about his own area of research expertise? Has he never encountered graduate students, post-docs, or mentors who would have corrected his misconceptions?
Here's the introduction to the interview,
Since the 1960s, it's largely been assumed that most of the DNA in the human genome was junk. It didn't encode proteins -- the main activity of our genes-- so it was assumed to serve no purpose. But Assistant Professor of Biology Nelson Lau is among a new generation of scientists questioning that hypothesis. His findings suggest we've been wrong about junk DNA and it may be time for a reappraisal. If we want to understand how our bodies work, we need to start picking through our genetic garbage.
BrandeisNow sat down with Lau to ask him about his research.
There's nothing wrong with being a "new generation" who questions the wisdom of their elders. That's what all scientists are supposed to do.
But there are certain standards that apply. The most important standard is that when you are challenging other experts you'd better be an expert yourself.
First off, what is junk DNA?
About two percent of our genome carries out functions we know about, things like building our bones or keeping the heart beating. What the rest of our DNA does is still a mystery. Twenty years ago, for want of a better term, some scientists decided to call it junk DNA.
Dan has already addressed this response but let me throw in my own two cents.
There was never, ever, a time when knowledgeable scientists said that all 98% of the DNA that wasn't part of a gene was junk. Not today, not twenty years ago (1996), and not 45 years ago.
There has never been at time since the 1960s when all non-gene DNA was a mystery. It certainly isn't a mystery today. If you don't know this then you better do some reading ... quickly. Google could be your friend, Prof. Lau, it will save you from further embarrassment. Search on "junk DNA" and read everything ... not just the entries that you agree with.
I added a bunch of links at the bottom of this post to help you out.
Is it really junk?
There’s two camps in the scientific community, one that believes it doesn’t do anything and another that believes it’s there for a purpose.
And you’re in the second camp?
Yes. It's true that sometimes organisms carry around excess DNA, but usually it is there for a purpose. Perhaps junk DNA has been coopted for a deeper purpose that we have yet to fully unravel.
It is possible that the extra DNA in our genome has an unknown deeper purpose but right now we have more than enough information to be confident that it's junk. You have to refute or discredit all the work that's been done in the past 40 years in order to be in the second camp.
Maybe when junk DNA moves to the right place in our DNA, this could cause better or faster evolution. Maybe when junk genes interacts with the non-junk ones, it causes a mutation to occur so humans can better adapt to changes in the environment.
Most of the undergraduates who took my course could easily refute that argument. I'm guessing that undergraduates in biology at Brandeis aren't as smart. Or maybe they're just too complacent to challenge a professor?
We've got a serious problem here folks. There are scientists being hired at respectable universities who aren't keeping up with the scientific literature in their own field. How does this happen? Are there newly hired biology professors who don't understand evolution?
Niu, D. K., and Jiang, L. (2012) Can ENCODE tell us how much junk DNA we carry in our genome?. Biochemical and biophysical research communications 430:1340-1343. [doi: 10.1016/j.bbrc.2012.12.074]
Doolittle, W.F. (2013) Is junk DNA bunk? A critique of ENCODE. Proc. Natl. Acad. Sci. (USA) published online March 11, 2013. [PubMed] [doi: 10.1073/pnas.1221376110]
Graur, D., Zheng, Y., Price, N., Azevedo, R. B., Zufall, R. A., and Elhaik, E. (2013) On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE. Genome Biology and Evolution published online: February 20, 2013 [doi: 10.1093/gbe/evt028
Eddy, S.R. (2013) The ENCODE project: missteps overshadowing a success. Current Biology, 23:R259-R261. [10.1016/j.cub.2013.03.023]
Hurst, L.D. (2013) Open questions: A logic (or lack thereof) of genome organization. BMC biology, 11:58. [doi:10.1186/1741-7007-11-58]
Kellis, M., Wold, B., Snyder, M.P., Bernstein, B.E., Kundaje, A., Marinov, G.K., Ward, L.D., Birney, E., Crawford, G. E., and Dekker, J. (2014) Defining functional DNA elements in the human genome. Proc. Natl. Acad. Sci. (USA) 111:6131-6138. [doi: 10.1073/pnas.1318948111]
Morange, M. (2014) Genome as a Multipurpose Structure Built by Evolution. Perspectives in biology and medicine, 57:162-171. [doi: 10.1353/pbm.2014.000]
I'm taking Ms. Sandwalk and hope to show her Down House. She loves old English houses.
She'll also be really excited to see Darwin's tomb in Westminster Abbey and tour the Natural History Museum. We'll make it a fun-filled week of science and evolution! Why don't you join us?
He brings up two points that are worth discussing.
What is a model organism?
There are two common definitions. Birney leans toward defining a model organism as one that models human biochemistry and physiology. This is a common definition. It emphasizes the meaning of "model" as "model of something."
Watch two medical educators from my Faculty of Medicine at the University of Toronto. They are being interviewed by Steve Paiken of The Agenda. They rightly deplore the traditional lecture style of learning that's common in my university but their solution is more online learning.
The real problem with medical education is that much of the first two years is based on the "memorize and regurgitate" model that we know is ineffective. The best way to change the system is to use evidence-based methods that emphasize student-based learning. The idea is to teach medical students how to access information and how to interpret it rather than have them memorize facts. When teaching biochemistry, for example, it's pointless to ask medical students to take an exam based on structures and pathways that they will forget the day after the exam.
These two physicians are in charge of reforming medical education. They want to please the students by creating a new way of teaching that emphasizes the way "millennials" want to learn. (Short online courses, no lectures.) You'll watch the entire show without hearing any references to the pedagogical literature and what's known to work. Is there any evidence that undergraduate medical students are experts on medical education? (Hint: ... no.)
If this is the wave of the future, I fear that future doctors are not going to be any more informed that the current crop. They will still not be capable of critical thinking.
The way we teach needs to change, but not this way.
We've known for a long time that the most common mistake is assuming that there's only one solution to a problem. They see an end result, like a bacterial flagellum, or resistance to malaria, or the binding of two proteins, and assume that a few very specific mutations had to occur in a specific sequence in order to produce that result.
judmarc calls this the "lottery fallacy" and I think it's a good term [see lottery fallacy],
This is of course what I like to call the "lottery fallacy." It's used by virtually every ID proponent to produce erroneously inflated probabilities against evolution.
Lottery fallacy: The odds against any *particular individual* winning the PowerBall lottery are ~175 million to 1. But there were three winners just last night. That's because *someone* winning the PowerBall is not an especially rare occurrence. It happens every few weeks throughout the year.
In exactly the same way, Axe, Gauger, Behe, and the rest of the ID folks always base their math on the chances that a *particular* neutral or beneficial mutation will occur, and just as with the lottery, the chances of a *particular* outcome are utterly minuscule. The occurrence of *some* neutral or beneficial mutation, however, is, as with the lottery, so relatively common as to be completely unremarkable.
To summarize: ID proponents misuse probability math to make the common appear impossible.
As it turns out, someone on Evolution News & Views (sic) just posted an excellent example of this fallacy [Intelligent Design on Target]. Here's what he/she/it says,
In his second major treatise on design theory, No Free Lunch: Why Specified Complexity Cannot Be Purchased without Intelligence, William Dembski discusses searches and targets. One of his main points is that the ability to reach a target in a vast space of possibilities is an indicator of design. A sufficiently complex target that satisfies an independent specification, he argues, creates a pattern that, when observed, satisfies the Design Filter. There are rigorous mathematical and logical proofs of this concept in the book, but at one point, he uses an illustration even a child can understand.
Consider the case of an archer. Suppose an archer stands fifty meters from a large wall with a bow and arrow in hand. The wall, let us say, is sufficiently large that the archer cannot help but hit it. Now suppose each time the archer shoots an arrow at the wall, the archer paints a target around the arrow so that the arrow sits squarely in the bull's-eye. What can be concluded from this scenario? Absolutely nothing about the archer's ability as an archer. Yes, a pattern is being matched; but it is a pattern fixed only after the arrow has been shot. The pattern is thus purely ad hoc. [No Free Lunch, pp. 9-10, emphasis added.]
Most people have experience with target shooting of some kind, whether with bows and arrows, guns (including squirt guns), snowballs, darts, or most sports like baseball, soccer, basketball, hockey, and football. Children laugh when they picture an archer who "couldn't even hit the broadside of a barn" and rushes up to the arrow and paints a bull's-eye around it. Grown-ups might compare that to a biologist looking at an irreducibly complex biological system and simply stating, "It evolved." In each of these cases, Dembski would say that since the pattern was not independently specified, therefore it is ad hoc.
Do you see the fallacy? Just because we observe a complex adaptation or structure does NOT mean that it was specified or pre-ordained. There are certainly many different structures that could have evolved—most of them we never see because they didn't happen. And when a particular result is observed it doesn't mean that there was only one pathway (target) to producing that structure.
To continue the analogy—at the risk of abusing it—there may be hundreds of targets in the woods and most of them have very large bullseyes. Imagine you're out for a walk in the woods and you see that almost every tree has a big target with a large bullseye. You find an arrow stuck at the edge of one of the bullseyes and lots of arrows stuck in the trees, the ground, and parts of most of the targets outside of the central bullseyes. Would you write a book about how good the archer must have been?
I've been trying to figure out why Intelligent Design Creationists are so excited about epigenetics. They seem to think it's going to overthrow everything we know about evolution (= "Darwinism"). That means, in their minds, that "naturalism" and "materialism" aren't sufficient to explain biology.
I'll just quote the relevant part and let you try and figure out whether Denyse represents mainstream Intelligent Design Creationism. 'Cause if she does, the movement is in far worse shape than even I imagined.
I remember one adoptive mother, taunted by a rebellious teenager who wanted to find her “real” mother, taking the girl by the shoulders and saying, “Look, I raised you from when you were seven days old; I supported you, sat with you in emergency rooms and juvenile court, laughed and cried with you, … and got you into a good school in the end. I don’t know who or where your birth mother is. But I do know this: I am the only ‘real mother’ you have ever had or ever will have. Look at me. Get used to it. It doesn’t GET better than this.”
I hope the kid smartened up. Meanwhile what if she discovers, when she has children, that their genome reflects in part traits she acquired growing up in the adoptive home? Maybe that would allay some of the sense of alienation.
Might epigenetics could provide some basis for understanding? Time will tell.
See also: Epigenetic change: Lamarck, wake up, you’re wanted in the conference room!
Vincent Torley read a post by Jerry Coyne where Jerry wondered if Intelligent Design Creationism was in trouble because the Discovery Institute has lost Bill Dembski and Casey Luskin [Is the Discovery Institute falling apart?].
Torley disagrees, obviously, but he focuses on a couple of the scientific statements in Jerry Coyne's post and comes up with Two quick questions for Professor Coyne.
I hope Professor Coyne won't mind if I answer.
Before answering, let's take note of the fact that Vincent Torley has been convinced by the evidence that most of our genome is junk. I wonder how that will go over in the ID community?
