Welcome to the 69th edition of the Carnival of Evolution! As February 12th was Darwin’s birthday, this is a Darwin’s Day carnival edition. To start with there’s a celebration of all things Darwinian at Synthetic Daisies, and a letter to the man himself for his 205th birthday.The next Carnival of Evolution will be at ????
Wow, I haven’t posted anything in quite a while. Things are busy outside blogoland. But committing this blog to the February edition of the Carnival of Evolution just made me do it, so here goes. We’ll do this by scales, bottom up.The next Carnival of Evolution (#70, April, 2014) will be at some unknown place.
One of the drawbacks of genome papers, however, is that they can create a mindset of sequence first, ask questions later. I once attended a Masters thesis defense where the external examiner asked the candidate why he sequenced the chloroplast genome of this particular species and what hypothesis was he trying to test. The student, looking startled, answered, "Because the genome hadn't been sequenced before and we didn't know what it looked like." After the defense, I overheard the examiner in the hallway venting to another professor. "We've created a culture of serial genomicists," she exclaimed. "Everyone's jumping from one genome sequence to the next, looking to score a major publication."I still like to read genome papers but lately I've been put off by the lack of reliable information in most of those papers. One of things I'm interested in is the number genes, especially the number of unique genes. Unfortunately, the annotation usually relies on computer-generated gene predictions and those are notoriously unreliable.
Regardless of this opinion, genome papers have provided much of the raw data that have shaped our view of genetics and evolution over the past 20 years. And they can also be a joy to read. Many of my favorite journal articles are genome papers. I remember, when I was a grad student in phycology, eagerly awaiting publication of the genome for Chlamydomonas—the superstar of green algae—and reading it incessantly once it was released, gleaning new insights each time through. There is something intimate and personal in learning about a species' genome. And similarly, if you are part of the team describing the genome, there is a feeling that you're giving the readers a first glimpse at an uncharted territory, with its unique landscape of genes, introns and intergenic regions.
But all of this may be coming to an end. Next generation DNA sequencing techniques have made it easy, fast and cheap to sequence genomes. Today, just about any scientist can walk out their laboratory doors, point to a living thing and say, “I will sequence you!” High-throughput technologies have flooded the academic market with genome papers. And the top journals have responded by only accepting papers describing the most novel, earth-shattering genomes. The less spectacular genomes, much like B-movies, go directly to video, or rather directly to GenBank. This sequencing-vs-publishing arms race has been going on for a long time.
...
Is it time to write the genome paper obituary? Maybe not quite yet. Every now and then they still claw their way into top journals. But the end is not far off, and when it does come, I'm sure that I speak for all of us genome geeks when I say, "Farewell, GP. It was fun while it lasted."
Smith, D.R. (2013) Death of the genome paper. Frontiers in Genetics 4:1-2. [doi: 10.3389/fgene.2013.00072]
Oh please. If there are any "creationists" out there who are running scared, they need not do so. The new article [by Chris Mooney] is titled "You Share 98.7 Percent of Your DNA with This Sex-Obsessed Ape," referring, of course, to the precious bonobo, a chimp-like ape famous for its progressive sexual habits. Just by itself, the genetic similarity between us and apes such as the bonobo is supposed to be of knockdown importance.This is a common argument from the IDiots. They assume that the intelligent designer created a model primate and then tweaked it a little bit to give chimps, humans, orangutans, etc. That's why the genomes of these species are so similar.
But what else would anyone expect, whether on a model of Darwinism, intelligent design, or creationism? Apes and humans are similar in many ways, and you don't need Darwinian evolution to see this.
Engineers can practice real science, but an engineer is not the same thing as a scientist. I agree that creationists can be perfectly good engineers, but how can you trust the scientific acumen of someone who insists that the earth is only 6,000 years old? That says right there that they have no respect for the evidence. How can Saletan ignore Ham’s bogus distinction between historical and observational science, in which he flatly rejects any possibility of inference about the past from the present? This creationism is utterly incompatible with biology, anthropology, geology, astronomy, climate science, geochemistry, cosmology, and any other science that deals with cause and effect and history. These sciences apparently do not matter to Saletan, as long as engineers make satellites and doctors do surgery.
Saletan cites Ham’s videos as falsifying the claim that creationism is incompatible with science. Ken Ham makes a big deal of this, too.
Oh for heaven’s sake! Engineers are scientists. Full stop. Are you really that desperate to deny that a creationist could ever make a contribution to science that you will sink to this level of insult and idiocy? (Yes, it is insulting to suggest that engineers are not scientists.)Engineers have a Bachelor's degree in engineering and they typically work for a construction company or in the IT department of a large corporation. They are not scientists. Full stop.
What is amazing is the evolutionist’s high confidence and self-assuredness in such a blatant misrepresentation of science. It would be difficult to imagine a bigger falsehood. Phylogenetic incongruence is rampant in evolutionary studies. Conflicts exist at all levels of the evolutionary tree and throughout both morphological and molecular traits. This paper reports on incongruent gene trees in bats. That is one example of many. These incongruences are caused by just about every kind of contradiction possible. Molecular sequences in one or a few species may be out of place amongst similar species. Or sequences in distant species may be strangely similar. As one paper admitted, there is “no known mechanism or function that would account for this level of conservation at the observed evolutionary distances.” Or as another evolutionist admitted, the many examples of nearly identical molecular sequences of totally unrelated animals are “astonishing.”
An even more severe problem is that in many cases no comparison is even possible. The molecular sequence is found in one species but not its neighbors. When this problem first became apparent evolutionists thought it would be resolved as the genomes of more species were decoded. No such luck—the problem just became worse. Not surprisingly evolutionists carefully prefilter their data. As one paper explained, “data are routinely filtered in order to satisfy stringent criteria so as to eliminate the possibility of incongruence.”
Short genes that produce what are known as microRNA also contradict Dawkins’ high claim. In fact one evolutionist, who has studied thousands of microRNA genes, explained that he has not found “a single example that would support the traditional tree.” It is, another evolutionist admitted, “a very serious incongruence.”
Another paper admits that “the more molecular data is analysed, the more difficult it is to interpret straightforwardly the evolutionary histories of those molecules.”
And yet in public presentations of their theory, evolutionists present a very different story. As Dawkins explained, gene comparisons “fall in a perfect hierarchy, a perfect family tree.” This statement is so false it isn’t even wrong—it is absurd. And then Dawkins chastises anyone who “could possibly doubt the fact of evolution.” Unfortunately this sentiment is typical. Evolutionists have no credibility.
L.A.: Knowledge in the real world does not entail either certainty or infallibility. When I claim to know that there is no God, I mean that the question is settled to my satisfaction. I don’t have any doubts. I don’t say that I’m agnostic, because I disagree with those who say it’s not possible to know whether or not God exists. I think it’s possible to know. And I think the balance of evidence and argument has a definite tilt.The argument from evil goes like this ...
G.G.: What sort of evidence do you have in mind?
L.A.: I find the "argument from evil" overwhelming — that is, I think the probability that the world we experience was designed by an omnipotent and benevolent being is a zillion times lower than that it is the product of mindless natural laws acting on mindless matter. (There are minds in the universe, but they’re all finite and material.)
I am a grad student, and long hours at the bench have got me thinking of other things lately, including the idea of marriage. I came up with a few criteria to direct me on my quest for a wife, and near the top of the list was that she needs to know what a gene is. I thought that this would be a reasonable thing to ask for. I like learning about how we and the rest of life work, and knowing how, in a general sense, cells are programmed to do what they do is a pretty good indicator of similar interest. My friends, however, disagreed with me, and on several occasions, as I shared my list, I feared that things were going to get violent. They argued that I will never get married with such a short-sighted and elitist attitude.Imagine that you would only seek partners who knew what a gene was. What definition would you require and why?
I read some newspaper articles, and some blog posts, that stated the obvious. It is totally wrong, all the time, to discriminate against someone based on their sexual preferences. If they use religion as an excuse then they should re-evaluate their religion. There is NEVER a time when an enlightened society should tolerate, let alone legalize, bigotry. I guess it's almost impossible to come out and say this on television, or maybe I'm just watching the wrong channels (mostly FOX and CNN).What I mean is that enlightened societies will almost always reach a consensus on discrimination against minorities. They will decide that society functions best when all types of discrimination are bad and should not be tolerated.
Notwithstanding any other provision of law, no individual or religious entity shall be required by any governmental entity to do any of the following, if it would be contrary to the sincerely held religious beliefs of the individual or religious entity regarding sex or gender: (a) Provide any services, accommodations, advantages, facilities, goods, or privileges; provide counseling, adoption, foster care and other social services; or provide employment or employment benefits, related to, or related to the celebration of, any marriage, domestic partnership, civil union or similar arrangement; (b) solemnize any marriage, domestic partnership, civil union or similar arrangement; or (c) treat any marriage, domestic partnership, civil union or similar arrangement as valid.In other words, if you are a bigot then the state will protect you from prosecution as long as you claim that your bigotry is based on religion.
First thing you have to know: the revolution is over. Neutral and nearly neutral theory won. The neutral theory states that most of the variation found in evolutionary lineages is a product of random genetic drift. Nearly neutral theory is an expansion of that idea that basically says that even slightly advantageous or deleterious mutations will escape selection — they’ll be overwhelmed by effects dependent on population size. This does not in any way imply that selection is unimportant, but only that most molecular differences will not be a product of adaptive, selective changes.The debate over adaptationism is a debate over mechanisms of evolution. Random genetic drift is a mechanism of evolution that results in fixation or elimination of alleles independently of natural selection. If there was no such thing as neutral mutations then random genetic drift would still be an important mechanism.
In recent years, RNA sequencing (RNA-Seq) has been favoured over microarrays. This new technology, using next-generation sequencing, is slightly more accurate, and nations have recently declared war over which is the best aligner to use.
In a recent poll, 98% of researchers answered "next-generation sequencing" to every single question – even their name, age and job title. The new science of "sequence first, think later" has been coined "nextgenomics".
I've exchanged many emails with brain surgeon and ENV contributor Dr. Michael Egnor, but I had never actually heard his voice till now. It's a good voice, which is vital for a physician, mellow yet authoritative, with the correct pitch and timbre. Egnor's stellar academic and medical background aside, I've often thought that, if you had no other information about a healthcare provider, what you don't want is a doctor with the wrong kind of voice.I'm disappointed that Egnor said nothing about me even though he posts quite a few comments on Sandwalk. Guess I don't get much respect.
Now you can hear Egnor as I just did in this fascinating new series of podcasts in which he is interviewed by Casey Luskin. Their themes include evidence of intelligent design in the complexity of the brain, but no less so in the simplest creature, a bacterium. Dr. Egnor compares that design to the solution of a Rubik's Cube. It doesn't happen by chance.
Egnor also talks about the unusual window that Jerry Coyne provides into the mind of a materialist, which is why his name comes up here often. Coyne, unlike many Darwin apologists, doesn't self-censor. You don't have to wonder: What does he really think about, for example, personal responsibility. Because he tells you! Whatever else Coyne may be, he's no weasel. For that, Egnor expresses his gratitude and -- yes, appropriately.
So, after all, that, let us return to Plait’s argument. He tells us that the problem is too many people perceiving evolution as a threat to their religious beliefs. Indeed, but why do they perceive it that way? Is it a failure of messaging on the part of scientists? Is it because Richard Dawkins or P. Z. Myers make snide remarks about religion? No, those are not the reasons.I hope Phil Plait is listening.
It is because these people have noticed all the same problems the scholars of Darwin’s time were writing about. It is because evolution really does conflict with their religious beliefs, but not because of an overly idiosyncratic interpretation of one part of the Bible. It is because the version of evolution that so worried the religious scholars of Darwin’s time, that of a savage, non-teleological process that produced humanity only as an afterthought, is precisely the version that has triumphed among modern scientists. And it is because the objections raised to that version of evolution in the nineteenth century have not lost any of their force today.
So I think the issue is just a tad more complex than Plait suggests. It manifestly is not the case that only the most narrow of fundamentalists has a problem with evolution. Evolution challenges the Bible, refutes the argument from design, exacerbates the problem of evil, and strongly challenges any notion that humanity plays a central role in creation. These are not small points, and Plait needs to acknowledge them.
For a number of years, many of us at UD have made the argument that evolutionary theory, in practice, is of almost no help whatsoever in getting at the secrets of biology. I’ve taken the position personally that it actually hurts, and that it is not a matter of indifference to the study of biology whether evolution is employed or not. ID is the way to go.Now, besides the fact that she is an IDiot, you may be asking why anyone would write such a thing.
They’ve studied this embryonic stage for 20 years, and couldn’t figure out the decisive signals for initiation of the gastrula. They had to look to “non-coding” RNA, i.e., “junk DNA,” in order to solve their new found secret.See? Evolutionary theory actually impedes scientific progress. And you wonder why we call them ....
And why didn’t they study “junk DNA” before? Well, evolutionary theory posits that it is “junk” (their word, not ours), so why investigate.
I can’t stress this enough. The conflict over the teaching of evolution is based on the false assumption that evolution is antagonistic to religion. This is why, I think, evolution is so vehemently opposed by so many in the United States. The attacks on the specifics of evolution—the claims about irreducibility of the eye, for example, or other such incorrect statements—are a symptom, not a cause. I can talk about how we know the Universe is old until the Universe is substantially older and not convince someone whose heels are dug in. But if we can show them that the idea of evolution is not contrary to their faith, then we will make far, far more progress.This is the classic accommodationist position. Problem is, it's been tried and it doesn't work in the United States. And the reason it doesn't work is that Americans aren't that stupid. They realize that these debates really are about science vs. religion. They know that evolution is, in fact, antagonistic to religion.
That’s not to say I’ll stop talking about the science itself. That still needs to be discussed! But simply saying science is right and faith is wrong will never, ever fix the problem.
And this won’t be easy. As long as this discussion is framed as “science versus religion” there will never be a resolution. A religious person who doesn’t necessarily think the Bible is literal, but who is a very faithful Christian, will more likely be sympathetic to the Ken Hams than the Bill Nyes, as long as science is cast as an atheistic dogma. For example, on the Catholic Online website, the argument is made that both Ham and Nye are wrong, and casts science as an atheistic venture.
That must change for progress to be made.
And who should do this? The answer to me is clear: Religious people who understand the reality of science. They have a huge advantage over someone who is not a believer. Because atheism is so reviled in America, someone with faith will have a much more sympathetic soapbox from which to speak to those who are more rigid in their beliefs.It's possible that "religious people who understand the reality of science" is a very small group and it's even more possible that they will be opposed to science and evolution precisely because they DO understand the reality of science. Plait is probably thinking about Ken Miller and Francis Collins but it's not clear to me that they truly understand what science is telling us. Science is telling us that there's no need for god(s) in order to understand the world around us. Evolution tells us that life has no purpose.
[Ruse] fails to grasp the real nature of the conflict. It's not just about evolution versus creationism. To scientists like Dawkins and Wilson, the real war is between rationalism and superstition. [my emphasis, LAM] Science is but one form of rationalism, while religion is the most common form of superstition. Creationism is just a symptom of what they see as the greater enemy: religion. While religion can exist without creationism, creationism cannot exist without religion.This passage has been widely quoted and I wholeheartedly agree with Coyne's view.1
1. There's some doubt about whether Coyne actually said this in his letter. I'm quoting a second-hand source: Dawkins in The God Delusion.
2. I'm not saying we are correct. I'm just saying that after all these years it's disappointing to see so many accommodationists who just don't get it.
The efforts of apologists to find genuinely distinguished modern scientists who are religious have an air of desperation, generating the unmistakably hollow sound or bottoms of barrels being scraped.Dawkins goes on to point out that efforts to find creationist Nobel Prize winners in Physics, Chemistry, or Physiology & Medicine have been largely unsuccessful.
RNA differs from DNA in one of the sugars that makes up its backbone and one of the bases that makes up its side branches (uracil instead of thymine); it is also usually found in single strands instead of DNA's double helix. New discoveries, though, are showing RNA does far more than passively transfer DNA's information to other places. It, too, is a masterpiece of intelligent design and function.
A paper in Nature describes how information is stored not only in RNA's base sequence, but in its folds. Because RNA has more degrees of freedom, it can take on a wide variety of forms not possible for DNA. "RNA has a dual role as an informational molecule and a direct effector of biological tasks. The latter function is enabled by RNA's ability to adopt complex secondary and tertiary folds and thus has motivated extensive computational and experimental efforts for determining RNA structures," the authors begin (emphasis added). In their conclusion, they say, "We identify hundreds of specific mRNA regions that are highly structured in vivo, and we show for three examples that these structures affect protein expression."
In other words, the structure, not just the sequence, carries functional information.Amazing. Sounds like they've never heard of the idea that ribosomal RNA catalyzes peptide bond formation and that it does so through secondary structure. They've never heard of self-splicing introns. All they have to do is read an introductory textbook of biochemistry or molecular biology.
More design found in what was formerly called junk; more information found parallel to existing information in RNA; more power found in the collective energy of intelligent agents. Why are you not surprised?The real question is why are IDiots surprised by routine information that even high school students know?
In the near decade that I’ve been watching the Intelligent Design movement, one thing has consistently amazed me: the pathological inability of many ID critics to accurately represent what ID actually is, what claims and assumptions are made on the part of the most noteworthy ID proponents, and so on. Even ID critics who have been repeatedly informed about what ID is seem to have a knack for forgetting this in later exchanges. It’s frustrating – and this from a guy who’s not even a defender of ID as science.I try really hard not to misrepresent the Intelligent Design Creationist movement. That includes my preference for adding the word "Creationist" to their label. What they're talking about is creationism—a being who creates the universe and who creates some aspects of living organisms.
Hat Tip: Jerry Coyne
In order for high school graduates to reach their full potential in life, they need to be:There's nothing radical about these goals. They're pretty much the same goals that any conference in the 1960s would have come up with. The only really new buzzword is "entrepreneurial"—that's borrowed from business and it wouldn't have been popular in the 1960s. Today every high school student has to be an entrepreneur because by 2030 nobody will be working for anyone else. They'll all be running their own businesses.1
- lifelong learners who can identify and synthesize the right knowledge to address a wide range of challenges in a complex, uncertain world
- literate, numerate, and articulate
- creative, critical thinkers
- able to collaborate effectively with others, especially those of different abilities and backgrounds
- open to failure as an essential part of progress
- adaptable and resilient in the face of adversity
- aware of the society they live in and able to understand the different perspectives of others
- self-aware and cognizant of their own strengths and limitations
- entrepreneurial, self-motivated, and eager to tackle the challenges and opportunities of their world
To achieve these goals, we require a radically di fferent structure for learning in 2030, one in which traditional concepts of classes, courses, timetables, and grades are replaced by more flexible, creative and student-directed forms of learning. This develops deep conceptual understanding, which can then be applied in other contexts.
1. This will save enormous amounts of tax dollars because nobody will be working for the government.
Science advances by discovering new things and developing new ideas. Few truly new ideas are developed without abandoning old ones first. As theoretical physicist Max Planck (1858-1947) noted, "A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it." In other words, science advances by a series of funerals. Why wait that long?There was a time—about a decade ago—when reading the answers to the question was exciting and stimulating.
WHAT SCIENTIFIC IDEA IS READY FOR RETIREMENT?
Ideas change, and the times we live in change. Perhaps the biggest change today is the rate of change. What established scientific idea is ready to be moved aside so that science can advance?
Epigenetic control of gene expression contributes to cells in a single organism (which share the same DNA sequence) developing differently into e.g. heart cells or neurons. But the last decade has shown actual evidence–and possible mechanisms–for how the environment and the organism's behavior in it might cause heritable changes in gene expression (with no change in the DNA sequence) that are passed onto offspring. In recent years, we have seen evidence of epigenetic inheritance across a wide range of morphological, metabolic, and even behavioral traits.If I had to give a reason why natural selection is not the only engine of evolution I would have picked something very different—something that's been around, and proven, for decades. Epigenetics requires DNA sequences and proteins and if epigenetic modification of a specific DNA site provides a selective advantage under some circumstances then that's natural selection in action.
The intergenerational transmission of acquired traits is making a comeback as a potential mechanism of evolution. It also opens up the interesting possibility that better diet, exercise, and education which we thought couldn't affect the next generation–except with luck through good example–actually could.
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At the first event of the series, Fr. Philip Cleevely (Catholic priest and philosophy professor) and Justin Trottier (founder of the Centre for Inquiry Canada) will argue the question, "Is There a God?" The debate will be moderated by Stephen LeDrew (host/commentator of CP24).
Date: Friday, February 7 from 7:00-9:30pm
Venue: Isabel Bader Theatre (Victoria University)
93 Charles Street West, Toronto
Registration: Limited seating. Tickets cost $10. Click here to register.
Biographies:
Fr. Philip Cleevely, C.O. was born in England in 1966. Educated in English Literature and Philosophy at Oxford and Cambridge Universities (UK) and in Toronto, he joined the Catholic Church in 1989. For years later, he entered a religious community in Birmingham, England called the Oratory of St. Philip Neri. Following theological studies in Rome, he was ordained to the priesthood in 2001. At the beginning of 2011, he transferred permanently to the Oratory community in Toronto, where he teaches Philosophy and Theology at St Philip’s Seminary.
Justin Trottier is Founder and Ambassador for the Centre for Inquiry Canada, an educational charitable organization advancing science and secularism. He is a board member of the Canadian Secular Alliance and a regular spokesperson on church-state separation, skeptical inquiry and fundamental freedoms. He hosts Think Again! TV, appears regularly on the John Oakley Show’s Culture War on AM640 Toronto radio and the Conspiracy Show on Vision TV, and publishes on the National Post’s religion blog. He ran as a candidate in the 2011 Ontario provincial election. With a passion for science education, Justin also hosts The Star Spot, a space sciences themed podcast and radio show
After-party:
After the event, all of our atheist, freethinking, and skeptical members, guests and friends are invited to join us at:Keep the discussion going on our Facebook Page.Gabby’s Bar & Grill
192 Bloor Street West
Toronto
ON M5S 1T8
Is there a God? Why is the majority of the global population religious (and why are some not)? Why does religious faith lead to resistance in the face of scientific evidence? Why are research findings in evolutionary biology and cosmology still contentious among the public, while those in chemistry and physiology are not? What are the implications of religious belief in scientific progress?
These are some of the questions we will delve into at our next Thoughts on Science (TOS) meeting. Individuals of all worldviews are encouraged to attend to enlighten and be enlightened.
1. That's -4°F if you live in Belize or the United States of America.
