…and this is a 
I've been giving talks at scientific meetings on educational outreach — I've been telling the attendees that they ought to start blogs or in other ways make more of an effort to educate the public. I mentioned one successful result the other day, but we need more.
I give multiple reasons for scientists to do this. One is just general goodness: we need to educate a scientifically illiterate public. Of course, like all altruism, this isn't really recommended out of simple kindness, but because the public ultimately holds the pursestrings, and science needs their understanding and support. Another reason, though, is personal. Scientific results get mangled in press releases and news accounts, so having the ability to directly correct misconceptions about your work ought to be powerfully attractive. Even worse, though, I tell them that creationists are actively distorting their work. This goes beyond simple ignorance and incomprehension into the malign world of actively lying about the science, and it happens more often than most people realize.
I have another painful example of deviousness of creationists. There's a paper I've been meaning to write up for a little while, a Nature paper by David and Alm that reveals an ancient period of rapid gene expansion in the Archaean, approximately 3 billion years ago. Last night I thought I'd just take a quick look to see if anybody had already written it up, so I googled "Archaean genetic expansion," and there it was: a couple of references to the paper itself, a news summary, one nice science summary, and…two creationist distortions of the paper, right there on the first page of google results. I told you! This happens all the time: if there's a paper in one of the big journals that discusses more evidence for evolution, there is a creationist hack somewhere who'll quickly write it up and lie about it. It's a heck of a lot easier to summarize a paper if you don't understand it, you see, so they've got an edge on us.
One of the creationist summaries is by an intelligent design creationist. He looks at the paper and claims it supports this silly idea called front-loading: the Designer seeded the Earth with creatures that carried a teleological evolutionary program, loading them up with genes at the beginning that would only find utility later. The unsurprising fact that many gene families are of ancient origin seems to him to confirm his weird idea of a designed source, when of course it does nothing of the kind, and fits quite well in an evolutionary history with no supernatural interventions at all.
The other creationist summary is from an old earth biblical creationist who tries to claim that "explosive increase in biochemical capabilities happened in anticipation of changes that were to take place in the environment", a conclusion completely unsupportable from the paper, and also tries to telescope a long series of changes documented in the data into a single ancient event so that they can claim that the rate of innovation was so rapid that it contradicts the "evolutionary paradigm".
So lets take a look at the actual paper. Does it defy evolutionary theory in any way? Does it actually make predictions that fit creationist models? The answer to both is a loud "NO": it is a paper using methods of genomic analysis that produce evolutionary histories, it describes long periods of gradual modification of genomes, and it correlates genomic innovations with changes in the ancient environment. It is freakin' bizarre that anyone can look at this work and think it supports creationism, but there you are, standard operating procedure in the fantasy world of the creationist mind.
Here's the abstract, so you can get an idea of the conclusions the authors draw from the work.
The natural history of Precambrian life is still unknown because of the rarity of microbial fossils and biomarkers. However, the composition of modern-day genomes may bear imprints of ancient biogeochemical events. Here we use an explicit model of macro- evolution including gene birth, transfer, duplication and loss events to map the evolutionary history of 3,983 gene families across the three domains of life onto a geological timeline. Surprisingly, we find that a brief period of genetic innovation during the Archaean eon, which coincides with a rapid diversification of bacterial lineages, gave rise to 27% of major modern gene families. A functional analysis of genes born during this Archaean expan- sion reveals that they are likely to be involved in electron-transport and respiratory pathways. Genes arising after this expansion show increasing use of molecular oxygen (P=3.4 x 10-8) and redox- sensitive transition metals and compounds, which is consistent with an increasingly oxygenating biosphere.
This work is an analysis of the distribution of gene families in modern species. Gene families, if you're unfamiliar with the term, are collections of genes that have similar sequences and usually similar functions that clearly arose by gene duplications. A classic example of a gene family are the globin genes, an array of very similar genes that produce proteins that are all involved in the transport of oxygen; they vary by, for instance, their affinity for oxygen, so there is a fetal hemoglobin which binds oxygen more avidly than adult hemoglobin, necessary so the fetus can extract oxygen from the mother's circulatory system.
So, in this paper, David and Alm are just looking at genes that have multiple members that arose by gene duplication and divergence. They explicitly state that they excluded singleton genes, things called ORFans, which are unique genes within a lineage. That does mean that their results underestimate the production of novel genes in history, but it's a small loss and one the authors are aware of.
If we were looking for evidence for evolution, we might as well stop here. The existence of gene families, for cryin' out loud, is evidence for evolution. This paper is far beyond arguing about the truth of evolution — that's taken for granted as the simple life's breath of biology — but instead asks a more specific question: when did all of these genes arise? And they have a general method for estimating that.
Here's how it works. If, for example, we have a gene family that is only found in animals, but not in fungi or plants or protists or bacteria, we can estimate the date of its appearance to a time shortly after the divergence of the animal clade from all those groups. If a gene family is found in plants and fungi and animals, but not in bacteria, we know it arose farther back in the past than the animal-only gene families, but not so far back as a time significantly predating the evolution of multicellularity.
Similarly, we can also look at gene losses. If a gene family or member of a gene family is present in the bacteria, and also found in animals, we can assume it is ancient in origin and common; but if that same family is missing in plants, we can detect a gene loss. Also, if the size of the gene family changes in different lineages, we can estimate rates of gene loss and gene duplication events.
I've given greatly simplified examples, but really, this is a non-trivial exercise, requiring comparisons of large quantities of data and also analysis from the perspective of the topologies of trees derived from that data. The end result is that each gene family can be assigned an estimated date of origin, and that further, we can estimate how rapidly new genes were evolving over time, and put it into a rather spectacular graph.
(Click for larger image)
Rates of macroevolutionary events over time. Average rates of gene birth (red), duplication (blue), HGT (green), and loss (yellow) per lineage (events per 10 Myr per lineage) are shown. Events that increase gene count are plotted to the right, and gene loss events are shown to the left. Genes already present at the Last Universal Common Ancestor are not included in the analysis of birth rates because the time over which those genes formed is not known. The Archaean Expansion (AE) was also detected when 30 alternative chronograms were considered. The inset shows metabolites or classes of metabolites ordered according to the number of gene families that use them that were born during the Archaean Expansion compared with the number born before the expansion, plotted on a log2 scale. Metabolites whose enrichments are statistically significant at a false discovery rate of less than 10% or less than 5% (Fisher's Exact Test) are identified with one or two asterisks, respectively. Bars are coloured by functional annotation or compound type (functional annotations were assigned manually). Metabolites were obtained from the KEGG database release 51.0 and associated with clusters of orthologous groups of proteins (COGs) using the MicrobesOnline September 2008 database28. Metabolites associated with fewer than 20 COGs or sharing more than two- thirds of gene families with other included metabolites are omitted.
Look first at just the red areas. That's a measure of the rate of novel gene formation, and it shows a distinct peak early in the history of life, around 3 billion years ago. 27% of our genes are very, very old, arising in this first early flowering. Similarly, there's a slightly later peak of gene loss, the orange area. This represents a period of early exploration and experimentation, when the first crude versions of the genes we use now were formed, tested, discarded if inefficient, and honed if advantageous.
But then the generation of completely novel genes drops off to a low to nonexistent rate (but remember, this is an underestimate because ORFans aren't counted). If you draw any conclusions from the graph, it's that life on earth was essentially done generating new genes about one billion years ago…but we know that all the multicellular diversity visible to our eyes arose after that period. What gives?
That's what the blue and green areas tell us. We live in a world now rich in genetic diversity, most of it in the bacterial genomes, and our morphological diversity isn't a product so much of creating completely new genes, but of taking existing, well-tested and functional genes and duplicating them (blue) or shuffling them around to new lineages via horizontal gene transfer (green). This makes evolutionary sense. What will produce a quicker response to changing conditions, taking an existing circuit module off the shelf and repurposing it, or shaping a whole new module from scratch through random change and selection?
This diagram gives no comfort to creationists. Look at the scale; each of the squares in the chart represents a half billion years of time. The period of rapid bacterial cladogenesis that produced the early spike is between 3.3 and 2.9 billion years ago — this isn't some brief, abrupt creation event, but a period of genetic tinkering sprawling over a period of time nearly equal to the entirety of the vertebrate fossil record of which we are so proud. And it's ongoing! The big red spike only shows the initial period of recruitment of certain genetic sequences to fill specific biochemical roles — everything that follows testifies to 3 billion years of refinement and variation.
The paper takes another step. Which genes are most ancient, which are most recent? Can we correlate the appearance of genetic functions to known changes in the ancient environment?
the metabolites specific to the Archaean Expansion (positive bars in Fig. 2 inset) include most of the compounds annotated as redox/e- transfer (blue bars), with Fe-S-binding, Fe-binding and O
2-binding gene families showing the most significant enrichment (false discovery rate<5%, Fisher's exact test). Gene families that use ubiquinone and FAD (key metabolites in respiration pathways) are also enriched, albeit at slightly lower significance levels (false discovery rate<10%). The ubiquitous NADH and NADPH are a notable exception to this trend and seem to have had a function early in life history. By contrast, enzymes linked to nucleotides (green bars) showed strong enrichment in genes of more ancient origin than the expansion. The observed bias in metabolite use suggests that the Archaean Expansion was associated with an expansion in microbial respiratory and electron transport capabilities.
So there is a coherent pattern: genes involved in DNA/RNA are even older than the spike (vestiges of the RNA world, perhaps?), and most of the genes associated with the Archaean expansion are associated with cellular metabolism, that core of essential functions all extant living creatures share.
Were we done then, as the creationists would like to imply? No. The next major event in the planet's history is called the Great Oxygenation Event, in which the fluorishing bacterial populations gradually changed the atmosphere, excreting more and more of that toxic gas, oxygen.
What happened next was a shift in the kinds of novel genes that appeared: these newer genes were involved in oxygen metabolism and taking advantage of the changing chemical constituents of the ocean.
Our metabolic analysis supports an increasingly oxygenated biosphere after the Archaean Expansion, because the fraction of proteins using oxygen gradually increased from the expansion to the present day. Further indirect evidence of increasing oxygen levels comes from compounds whose availability is sensitive to global redox potential. We observe significant increases over time in the use of the transition metals copper and molybdenum, which is in agreement with geochemical models of these metals' solubility in increasingly oxidizing oceans and with molybdenum enrichments from black shales suggesting that molybdenum began accumulating in the oceans only after the Archaean eon16. Our prediction of a significant increase in nickel utilization accords with geochemical models that predict a tenfold increase in the concentration of dissolved nickel between the Proterozoic eon and the present day but conflicts with a recent analysis of banded iron formations that inferred monotonically decreasing maximum concentrations of dissolved nickel from the Archaean onwards. The abundance of enzymes using oxidized forms of nitrogen (N2O and NO3) also grows significantly over time, with one-third of nitrate-binding gene families appearing at the beginning of the expansion and three-quarters of nitrous-oxide-binding gene families appearing by the end of the expansion. The timing of these gene-family births provides phylogenomic evidence for an aerobic nitrogen cycle by the Late Archaean.
So I don't get it. I don't see how anyone can look at that diagram, with its record of truly ancient genomic changes and its evidence of the steady acquisition of new abilities correlated with changes in the environment of the planet, and declare that it supports a creation event or front-loading of biological potential in ancestral populations. That makes no sense. This is work that shouts "evolution" at every instant, yet some people want to pretend it's an endorsement of theological hocus-pocus? Madness.
Scientists, you need to be aware of this. The David and Alm paper is an unambiguously evolutionary paper, using genomic data to describe evolutionary events via evolutionary mechanisms, and the creationists still appropriate and abuse it. If you publish anything about evolution, be sure to google your paper periodically — you may find that you've been unwittingly roped into endorsing creationism.
David LA, Alm EJ (2011) Rapid evolutionary innovation during an Archaean genetic expansion. Nature 469(7328):93-6.
Life Science
Comments
Posted by: Dhorvath, OM
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April 27, 2011 1:21 PM
That is so cool. It reminds my little uneducated brain of that evolution game you had a while back. (Yes,I am sure the intent was for things to work the other way, but such is my life.)
Oxygenation in the Archean seas has always seemed fascinating to me because of the geologic records, it's interesting to see it reflected in the gene records.
Posted by: Brother Ogvorbis, Apropos of Nada
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April 27, 2011 1:25 PM
Dr. Myers, you only have to look at the paper through eyeglasses made out of specially clarified Bibles and then this paper will suddenly make sense as a full-throttle support of CREATIONISMISM!!1!!!
An excellent explanation of the paper on your part. There is no way that I (keep in mind, I'm a public historian) would have been able to grock in fullness. (I kinda wish I were in late high school -- I'd apply to UM-Morris (still as a history major) but I suspect I would really enjoy your bio classes.)
Posted by: Enhizer
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April 27, 2011 1:33 PM
I love seeing that the fossil record, geochemical record, and gene records can all be linked together. Glad I took some inorganic courses that were not required for my biochemistry and microbiology degrees.
Posted by: Brownian
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April 27, 2011 1:35 PM
What's the deal with all that genetic loss (shown in yellow)?
Are those all T. Rex genes for digesting coconut milk lost in the Fall?
Posted by: Glen Davidson
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April 27, 2011 1:44 PM
What have they ever done, what can they ever do, but point to evolutionary evidence and try to fit it into some idiotic creationist scenario or other? Front-loading just being one of the more pathetic attempts to co-opt science.
Yeah, because the evolution of humans from fish is trivial.
Oh, except that it requires the intervention of Gawd, because no way can intelligence actually evolve due to front-loading.
Glen Davidson
Posted by: janiceclanfield
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April 27, 2011 1:51 PM
Ignore the creotards.
They're just jealous 'cause they don't have pretty graphs.
Posted by: RFW
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April 27, 2011 1:56 PM
There's one word in my vocabulary to describe these creationist lies: disgusting. Disgusting that presumably intelligent people should be so desperate to prop up fairy tales and arrant nonsense, and thereby abdicate their claim to be called "intelligent."
But there's a mystery here: what is the motivation for these lies? Is it just preaching to the choir that results in the liar having a feel-good experience? Or is it, as I so often suspect, because it keeps up the copious flow of dollars into the liars' pockets from the poor, disinformed members of their flock? Anybody have a clue?
Posted by: raven
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April 27, 2011 1:57 PM
Front loading can't work.
The mutation rate is way too high. Any genes waiting around for something to do would quickly end up mutated to oblivion.
The antarctic fish wihout hemoglobin or red blood cells, icefish, are only about 10 million years old. Already they have lost one globin gene completely and the other is just a fossilized wreck.
Same thing with the receptors in the vestigal human vomeronasal organ. They are still there. None of them work anymore.
Posted by: Blattafrax
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April 27, 2011 1:58 PM
Good paper; good post.
You mention the scale on the time axis, but what struck me was the other scale. At no time did the number of 'events' exceed 10 per genome per million years. Presumably averaged-out a'la punctuated equilibrium, but still a tiny rate on a human (or drosophila or bristlecone pine) life-time scale.
The rate of gene 'birth' was way more than I would have thought too. I had always assumed a common ancestor for most genes - or at least that the duplication rate would always be higher than the birth. Ho hum.
And oxygen usage gene evolution - neat!
Posted by: daniel.gaston
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April 27, 2011 2:00 PM
PZ, you might want to refresh your knowledge of the Eukaryotic Tree of Life, major groups, and the evolution of multi-cellularity if one of your examples for dating the origin of a gene family is something found in "Plants, Animals, and Fungi which then had to arise sometime after the origin of multi-cellularity."
The Protists are NOT a monophyletic group on the Eukaryotic tree, even the Wikipedia entry for Eukaryotes is somewhat up to date with regards to the 5/6 Supergroups and general arrangement of them on a tree. `It's bad enough this stuff is still taught wrong in high school and even university level intro biology courses, but science bloggers who specialize in evolution should know better.
Plants, Fungi, and Animals all have independent origins of multicellularity, although it appears that they probably used a lot of the same pieces from their genetic toolkit to do so. Each of these groups has unicellular groups that are more closely related than any of these multicellular groups are too each other, including Animals/Fungi which are fairly closely related to one another.
And of course there are other multicellular groups, like the brown algae, that have evolved from other major eukaryotic groups that are even more distantly related.
Posted by: tomhuld
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April 27, 2011 2:18 PM
I've been wanting to ask this for some time, but it was never on-topic: is there a good non-technical overview of the topic of gene families and the genealogy of genes? I tried Google, but all the most obvious search words return a garbage truck full of sites for researching your own genealogy. I think this is one of the most exciting new (at least to me) discoveries in genetics.
Posted by: Notta
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April 27, 2011 2:21 PM
I'm the director of outreach for a large research university. My university has made a financial commitment to its faculty to provide programs and audiences to promote interactions between research scientists and the general public. Blogs are fine, but most people aren't going to be surfing around the internet, looking for interesting takes on scientific phenomena or reading a layman's version of new research findings. You need to reach out to schoolchildren and school teachers to improve science literacy, and you can't just expect each scientist to go out on his or her own and find a way to reach out to the public. Frequently, you have to bring the public to the scientist, which is what the majority of my programs do by bringing students, teachers, and the public at large to events and programs on campus. The other half of the time, we're in the schools, promoting science instruction, investigations, and bringing kids in contact with practicing scientists. I would encourage anyone interested in outreach to read "Scientists in Science Education", written jointly by BSCS and the NIH Office of Science Education: "Scientists in Science Education"
Posted by: Spamamander, internet amphibian
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April 27, 2011 2:27 PM
I am baffled yet again by the ability of creationists to completely disregard the obvious and even outright lie about what they see. I probably shouldn't be, but I guess I just don't have the ability to not-think in such amazing ways.
I'm anything but a scientist; I'm a high school graduate (who happens to read Dawkins and Gould for fun) but looking at that graph I can see... EXACTLY what might have been predicted to happen! It's a beautiful fit showing the timing of gene tree development and then diversity arising from them. Isn't that how science is supposed to work? Posit a hypothesis based on observations, then run the tests to see if it holds true? Then again I'm probably not as edumacated as them there ID people.
Posted by: ritchie.annand
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April 27, 2011 2:34 PM
Daniel -> That was the one thing that jumped out at me about the posting, too. Choanoflagellates are a primitive cousin of sponges, and by no means does that split enrobe the origins of multicellular fungi or plants.
Other than that, a really fine analysis :)
Posted by: daniel.gaston
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April 27, 2011 2:47 PM
@ritchie.annand : Well I wouldn't say primitive. They are a close, unicellular relative of the metazoans. But that doesn't make them primitive. And of course the Plantae are even further removed from Animals and Fungi.
Posted by: Midnight Rambler
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April 27, 2011 3:02 PM
Very, very cool paper - brings together so much stuff into one piece. Thanks for posting on this, otherwise I probably would have missed it.
Posted by: Enkidum
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April 27, 2011 3:23 PM
Can anyone give me a relatively coherent explanation (or point me to one) of why new genes are effectively no longer being made (if I understood the article summary correctly)?
Is it because they existing genes out-compete them? Or am I just misunderstanding?
Posted by: David Marjanović
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April 27, 2011 3:25 PM
How was the dating done? How was it calibrated?
No. As his reading comprehension shows, he's not an intelligent {design creationist}. He's an {intelligent-design} creationist of the usual stupidity.
Some most likely are in it just for the money. But most, I'm sure, are first and foremost lying to themselves: they're afraid of hell, and therefore they're scared shitless of every tiny little doubt they ever have, so they try to brainwash themselves into believing that 2 + 2 = 5 when the Bible says so.
...and if you include all green algae in "plants", plants have several independent origins of multicellularity all of their own!
Yeast, BTW, is a secondarily unicellular mushroom. (OK, some yeasts are unicellular; others, like Candida, aren't.) Whenever you hear a molecular biologist say "higher eukaryotes" ( = all except yeast), jump at me and hold me, lest I commit irrational destructive acts.
Plants and brown algae are probably marginally more closely related to each other than to animals and fungi and slime molds*.
Oh, and, I almost forgot the actinomycetes: multicellular bacteria.
* One or two more independent origins of temporary multicellularity.
Try "phylogeny" instead of "genealogy".
Link doesn't work. Please try again. The quotation marks about the URL are not optional, and the http:// isn't either.
Of animals as a whole, not sponges alone.
Posted by: Horace
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April 27, 2011 3:27 PM
On the same site see:
http://askwhy.co.uk/dinosauroids/?p=569
Interesting material about race and evolution. Says a number of the things that Cochrane's the 10 000 year explosion says.
Posted by: daniel.gaston
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April 27, 2011 3:29 PM
@David: Plants and brown algae are probably marginally more closely related to each other than to animals and fungi and slime molds*.
Indeed, but like you said, only marginally. If the unikont/bikont split is "true" evolutionarily/phylogenetically than we would certainly consider them more closely related. But stramenopiles contain a whole whack of quite diverse organisms all their own.
Posted by: Ewan R
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April 27, 2011 3:35 PM
I get some funny looks in meetings when I point out that terms like higher and lower organism (plant generally, although also to refer to bacteria in general) are simply horrid. Hopefully one day the message will sink in, although thus far pouting doesn't seem to be doing the trick.
Posted by: David Marjanović
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April 27, 2011 3:36 PM
That probably happens, but I bet the distinction between "gene birth" and "gene duplication" is largely artificial: the farther back a duplication lies, the more difficult it is to recognize as such.
Genes do sometimes arise "out of nowhere". The antifreeze proteins of the abovementioned icefishes have mutated out of junk DNA. But this is very rare, and Archaean organisms probably had very little junk DNA in the first place.
Posted by: Peter Ashby
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April 27, 2011 3:40 PM
Celebrate the Archaean Expansion! for that was when genes involved in metabolizing alcohol were born, stopping it being a poison. Raise a glass to that fact tonight.
Posted by: mbadmin
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April 27, 2011 3:41 PM
While I was never personally religious, the need for science explained is huge. I think that good science for the masses is crucial if we ever want to break the grip of mysticism.
As Joe Average this blog is always my first or second stop during the day. While I come for the blog, the commenters are the added treat.
Posted by: Earthltd
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April 27, 2011 3:44 PM
Love that science!
Did you see the faces first or the vase?
Posted by: Horace
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April 27, 2011 3:44 PM
@17
>Can anyone give me a relatively coherent >explanation [...] of why new genes are >effectively no longer being made [...]?
>Is it because they existing genes out-compete >them?
I think that you are right, there was less competition at the start of the Archean explosion as gene function had not been improved through evolution. It was thus possible for there to try a number of different solutions for any biochemical problem.
Imagine a field with various hills in it. You pick several spots at random and then try to move to higher ground (i.e. increasing the efficiency of what ever version of the gene you are using).
As evolution forced the genes "uphill", gradually improving their function, only the solutions with the highest genetic peaks survived.
Posted by: kieran
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April 27, 2011 3:48 PM
I came across an article while debating a creationist. http://www.icr.org/article/5522/ Now I always check the references on a creationists article. It amazing what gets left in there. I found that the first reference was to a lecturer from my own college http://www.scientificamerican.com/article.cfm?id=winged-victory
Sent on the ICR article and he was supirsed that it could be spun that way!
Posted by: David Marjanović
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April 27, 2011 3:53 PM
Huh? I mean "around".
Darwin himself wrote "say never higher or lower" into the margins of a book in, what, 1844?
But that's not even what I mean. I mean that "higher eukaryotes", as the term is used by so many molecular biologists, describes a screamingly paraphyletic assemblage and implies a mind-bogglingly crazy phylogeny.
...while the metaphorical landscape kept changing at random due to metaphorical tectonics, metaphorical erosion, metaphorical glaciations (hey, non-metaphorical Snowball Earth events for instance), and so on...
Posted by: Peter Ashby
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April 27, 2011 3:55 PM
Another method for 'novel' genes is things like transposons and funky chromosomal crossover events that scramble genes so bits of one get mixed up with bits of other genes. Many genes have regions that are recognisably from different gene families. Extracellular matrix receptors are classic for this. You think immunoglobulins are immune system stuff? Nope, not only anyway. Once you have invented a good sticky thing you can use it anywhere you need a sticky thing to stick to another sticky thing.
Gene maps where the protein has been analysed will have little boxes around regions showing the origin of all the parts. Family relationships are in parts as well as wholes.
Posted by: CJO
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April 27, 2011 3:59 PM
they're afraid of hell, and therefore they're scared shitless of every tiny little doubt they ever have, so they try to brainwash themselves into believing that 2 + 2 = 5 when the Bible says so.
Maybe this is just another way of conceptualizing being "afraid of hell" (I wouldn't know, since that fear is so utterly foreign to me), but I think they're more afraid of a here-and-now universe that doesn't have a cosmic overlord who behaved in the past in the ways the Bible said he did, such that Jesus's salfific sacrifice has no meaning. It's a sunk costs thing. They're so committed to their pat narrative of creation, sin, death, redemption that the open-ended and provisional nature of an evolutionary origin for humanity is terrifying even without the implications for the afterlife, or what have you. It. can. not. be. true. else there is no meaning or value to anything. So, yeah, a lot of them believe the lies they tell.
Posted by: Ewan R
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April 27, 2011 4:02 PM
Clearly the noachian flood is what wiped out all the genes on the low peaks!
Posted by: James F
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April 27, 2011 4:11 PM
I ain't never seen nobody give birth to a gene!
Posted by: Blattafrax
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April 27, 2011 4:22 PM
What David M said. Plus also remember that these are gene families that are being discussed. Individual examples within the family can be created, lost, modified to deal with specific situations, but on the whole, the families deal with big problems: 'Is there a nutrient out there?' 'What to do with all this oxygen?' 'Replicate DNA accurately'. Nothing much has changed at that level since multicellular life evolved.
Unless our oceans become 21% fluorine or the license expires on our use of the mRNA patent, I wouldn't expect anything new too soon. With our planet's current equilibrium, tinkering with what's already there is enough.
Posted by: F
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April 27, 2011 4:58 PM
Oh, this looks positively tasty. Now I'm gonna read it. Nom nom.
Posted by: joed
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April 27, 2011 5:06 PM
"Of course, like all altruism, this isn't really recommended out of simple kindness..."
Professor Myers, if you have never done something for another human simply out of kindness then you haven't lived!
Your quoted statement here sounds like something Ayn Rand would teach you and you would profess her teaching. And I am pretty sure you are not an Ayn Rand fan, but I could be wrong.
Posted by: https://me.yahoo.com/a/O.jullMj0I2VvJaxMMVeNKSfOPf73voLSxJAe9PdlOWwi8Y-#258ec
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April 27, 2011 5:19 PM
I think one of the most amazing, humbling and exalting things to realize for me is that our present atmosphere is derived by the biological processes of the life that exists on earth. That the process can be tracked in the mineral deposits found and exploited by us is remarkable and that it can also be tracked in the genetic makeup of that life wonder filled
thanks for the "digest" of the paper!
uncle frogy
Posted by: F
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April 27, 2011 5:21 PM
Typo:
Iiiiiiii like it!
Posted by: Ichthyic
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April 27, 2011 5:24 PM
I ain't never seen nobody give birth to a gene!
probably because you weren't invited to witness the birth of anyone named Gene?
Posted by: redmjoel
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April 27, 2011 5:27 PM
This is one of the problems with the modern journal system. You are unable to vet the sources of these people unless you have access to the journals, which most non-academics don't due to the high cost. Blogs can go a long way to filling the gap.
In some ways scientists are in as much of an echo chamber as the creationists and the wingers. They speak to each other in their own language, in their own journals, etc.
Popular science books, Scientific American, etc. lets some of the science filter out to the general public, but not enough, and then it's mostly conclusions, not evidence. Sitting next to Scientific American on every shelf is Discover, which IMHO publishes as much pseudoscience as science.
For instance, I still haven't seen a good introduction to the science of (and evidence for) climate change for a general audience. I've been able to find the IPCC paper, but not much beyond that. Lacking this in a collated form makes it much easier for denialists to get a foothold. The same can be said for vaccine research, which sounds a lot like homeopathy until you dig in a bit further. Dawkins recent book is a stellar example of the kind of outreach needed on may of these "controversial" scientific issues.
This isn't to say there aren't good reasons for science literature being what it is, but it is still the case. Nor am I saying that the science should be dumbed down. It's just that much of it is inaccessible to general audiences.
Posted by: Alex, adv. diab.
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April 27, 2011 5:30 PM
I swear, the cdesignproponentists saw the word "Surprisingly" in the abstract and thought to themselves - The scientists are baffled! Therefore evolution is wrong! God did it!
Thanks for the analysis, I can go to bed now feeling a little more educated!
Posted by: Sid Leminov
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April 27, 2011 5:39 PM
Do you know the Copenhagen Diagnosis? (Or is that what you meant by 'the IPCC paper'?)
Posted by: F
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April 27, 2011 5:44 PM
Are you kidding? Been to a library or the internet?
One-off minor example: http://www.realclimate.org/
Posted by: redmjoel
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April 27, 2011 5:44 PM
@Sid Leminov: I was actually referring to the precursor paper, AR4. This looks interesting ...
although $50 feels a bit steep. Meh, I'll think about it.
Posted by: maglione.k
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April 27, 2011 5:56 PM
On the one hand, yay for not being too much of a coward to link to your opponents. On the other hand, argh, you had to go and add to their already horrifically inflated Page Rank.
Posted by: Timberwoof
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April 27, 2011 5:58 PM
WTF? I posted this here and it ended up over there. I try again:
Clearly something is going on in the biosphere now, with all the increases in floods, droughts, fires, and whatnot. Whether you attribute it to global warming or the Coming of the Horsemen*, surely Yahoo would be preparing the flora and fauna for the coming calamity. Do any biologists, real or imagined (meaning Biblical), report any such anticipatory increases in species diversity? Anyone? Anyone?
The sound of crickets is so soothing.
* Why does that sound like the title of a porno film?
Posted by: 'Tis Himself, OM
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April 27, 2011 6:04 PM
Thanks for the explanation, PZ. Also thanks to all the biologist commentators for expanding the explanation. I feel less iggerant than I did previously.
Posted by: Amphiox, OM
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April 27, 2011 6:19 PM
Ah, but there you have it in a nutshell. For at the very least the altruistic act gets rewarded with the feel-good thrill of doing something good for another human!
And thus all altruism is done for at least one reason more than just simple kindness!
Posted by: hje
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April 27, 2011 6:20 PM
I sometimes think it might be worthwhile to have an crowd sourced effort to do what PZ has done here with just one aspect of the creationist disinformation campaign: to have a web site that rapidly refutes every bit of nonsense as it appears on AIG and the like.
Of course it would be a Sisyphean task requiring lots of energy that could be put to more useful ends, like learning more about how the universe actually works.
Posted by: redmjoel
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April 27, 2011 6:28 PM
@F: No, not kidding, but thanks for the pointer.
Posted by: Ichthyic
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April 27, 2011 6:30 PM
I sometimes think it might be worthwhile to have an crowd sourced effort to do what PZ has done here with just one aspect of the creationist disinformation campaign: to have a web site that rapidly refutes every bit of nonsense as it appears on AIG and the like.
I thought there already was?
http://www.talkorigins.org/indexcc/
Posted by: MrFire
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April 27, 2011 6:32 PM
BUT WERE YOU THERE?
Posted by: joed
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April 27, 2011 6:56 PM
amphiox not you too! another Ayn Rand fan.
Ascribing motive to self or others can be nothing more than a guess when it comes to altruism. Gosh, we can't even know our own motives for sure. but it makes some people feel good or important or superior etc to think they know why someone did a kind/evil act.
So, if you can't do a kind act without some motive other than kindness, or even with any motive, then too bad. It's like being very proud of how humble you are. Wow, not healthy, but typical.
Posted by: Menyambal: Making sambal (it isn't dragon magic).
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April 27, 2011 7:05 PM
No, I wasn't there, but my ancestors were.
Great post, PZ!
Posted by: eastsidepropjoe
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April 27, 2011 7:22 PM
Yep.. those creationists got two results on the first page for a query almost no one would ever submit. Quite a coup.
(BTW, I don't see any creationist results, FWIW.)
Posted by: Jeanette Garcia
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April 27, 2011 7:36 PM
I love it when you talk science PZ. Evolution is so much more interesting and mind expanding than creationist fairy tales. I don't understand what happened to education in this country. Where is the curiosity?
Posted by: kev_s
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April 27, 2011 7:38 PM
Scientific papers on evolution need to include a statement like: "Nothing in this paper can be interpreted as supporting creationism, intelligent design, or any similar non-scientific idea that may evolve from those ideas in the future".
Posted by: Nerd of Redhead, OM
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April 27, 2011 7:45 PM
Well explained review PZ. Very interesting work.
Posted by: john.marley
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April 27, 2011 8:04 PM
@joed
Talk a lot, don't you.
Posted by: Timberwoof
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April 27, 2011 8:28 PM
"I sometimes think it might be worthwhile to have an crowd sourced effort to do what PZ has done here with just one aspect of the creationist disinformation campaign: to have a web site that rapidly refutes every bit of nonsense as it appears on AIG and the like."
http://rationalwiki.org/wiki/Main_Page addresses part of this.
Posted by: Kevin
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April 27, 2011 8:43 PM
@35...Try Dennett's "Freedom Evolves" for a thorough dissection of the problems in even describing altruism.
I'm on page 201 as we speak...not that I subscribe to every argument Dennett makes (does that make me a HERETIC?), but it's 100% on-point with regard to altruism.
Posted by: Markita Lynda: Healthcare is a damn right
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April 27, 2011 9:02 PM
I love how the evolutionary pattern of "branch, then prune" crops up at all scales, from single populations to this vast sweep of eons.
Posted by: etherraichu
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April 27, 2011 9:18 PM
A lot of people seem to have this all-encompassing fear of science. Its difficult to explain.
Every day we see people call into questions effects that their computer couldnt run without.
Every day I see yet another idiot who thinks that vaccines are a conspiracy to give people autism...so the pharmaceuticals can make huge profits off the vaccines.
..Yeah, it makes no sense; But heres where it gets creepy: A significant number of such people do not understand genetic heredity. They just dont. I have heard wonderful phrases like "Evolution cant make bad traits, since anyone with the trait would die!"
When someone says they talk to "experts" and that those "experts" told them this stuff, they hate having it asked what expert said this, and why they would take the time to explain something to an idiot who spends all day arguing on the internet?
This is what the dumbing down of our populace gets you. People afraid of magic, threatening to kill because they think we have magic powers.
And you get conspiracies: These vaccine idiots, for instance, will claim the CDC said it was true, and deamnd you watch a video where it says nothing of the sort. You send them a link to the CDC where it does a line by line review of each ingrediant; the idiots scream that 'its not just mercury' and clearly didnt read anyhting.
And nowadays, they are claiming that every health body in the entire world is in on the conspiracy, because theyve all corrently pointed out these people are insane and stupid and ask for antibiotcs for a cold.
These fools are the ones I know best, but its not just them; its gotten to the point where people cannot, in any way, filter trut hfrom fiction. And thats why we get real life riots over fantasy states.
These groups will eventually claim that despite these conspiracies being SO powerful, they cant stop the dang youtube idiots from telling everyone.
We are dealing with stupid beyond beliefe, beyond explination. And it comes in every field; im sure anyone else in any science has heard very much like what I have above. It never stops and its getting really tiring. How can we explain why we need funding when the idiots don't know why you'd want to monitor volcanoes?
Posted by: Kel, The Privileged View From Nowhere
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April 27, 2011 9:19 PM
A few anecdotes.
A couple of years ago I went to a public lecture at ANU where the geneticist there was talking about the genome of the platypus and how badly it was designed. She mentioned when the paper was published in Nature, the Discovery Institute gave a press release about the platypus being evidence of intelligent design. Upon hearing about this, her reaction was 'that's the stupidest thing I've ever heard.
I remember seeing a creationist try to argue that Tiktaalik wasn't a transitional fossil and cited a Nature paper that backed this up. I tracked down the paper and read it, and in no way did it indicate that Tiktaalik wasn't a traditional form, but that it wasn't likely to be ancestral to tetrapods.
And yet in another creationist assertion about a paper in Nature, a peper that looked as causes of speciation showed the role of chance geographical events as playing a major role as opposed to natural selection pulling lineages two different ways. Upon reading the paper (and listening to one of the authors talk about iit on the Nature podcast) I was baffled as to how it could be taken as a paper against evolution.
The point I'm trying to get
Posted by: Kel, The Privileged View From Nowhere
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April 27, 2011 9:24 PM
Damn it, hit submit too soon...
The point I'm trying to get at is that creationists are going to try to take any finding and twist it in such a manner that casts doubt on the validity of evolution - either that the case isn't as strong as they make it out to be or that it supports a divine conclusion. The only solution is to make sure every paper abstract carries the label 'This paper does not support the notion of intelligent design, and is perfedctly consistent with the fact of evolution'.
Posted by: joed
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April 27, 2011 10:01 PM
@john.marley
NON!
Posted by: Haltz
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April 27, 2011 10:07 PM
Great teaching in this post. But I have a question about the point of which it is an illustration, i.e., the need for scientists to blog and explain their work: Would the people who are so vulnerable to the lies and mischaracterizations of the research spread by the creationists be likely readers of the blogs that explain that research? This question in no way diminishes either the value of PZ's suggestion, or the value of such explanations for the rest of us who need such "popularizations" of the sometimes very technical research publications. Just asking.
Posted by: Amphiox, OM
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April 27, 2011 10:12 PM
I'm sorry, joed, but I'm afraid I have absolutely no idea what you're talking about here. I despise everything about Ayn Rand. (except for the fact that her writings inspired the development of a kickass video game by the name of BioShock).
No, no, no, no, no, no! I'm saying that real humans (not hypothetical fictional ones) don't (not can't) do kind acts without other motivations in addition to kindness. Because real humans never do anything without only a single motivation!
Posted by: Lyn M: Just Lyn M.
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April 27, 2011 10:22 PM
@ Haltz #66
If scientists blog, then you get to read about real research and real results from an expert. You can then use that information when you do run across the vulnerable who are, if only for a moment, thinking about things. Further, you have another place to send them for information.
Seeing that science is real, is happening right now, and is about things that people need to know, well that is a great gift to all of us. Having lots of such sites can only help.
And think of this, if such sites do nothing, why do the religious folks spend so much time setting such sites up and spreading links around? It helps to create the feeling that their stuff is somehow "real" and represents the majority. Let's show them real.
Posted by: Lyn M: Just Lyn M.
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April 27, 2011 10:26 PM
@ Haltz #66
If scientists blog, then you get to read about real research and real results from an expert. You can then use that information when you do run across the vulnerable who are, if only for a moment, thinking about things. Further, you have another place to send them for information.
Seeing that science is real, is happening right now, and is about things that people need to know, well that is a great gift to all of us. Having lots of such sites can only help.
And think of this, if such sites do nothing, why do the religious folks spend so much time setting such sites up and spreading links around? It helps to create the feeling that their stuff is somehow "real" and represents the majority. Let's show them real.
Posted by: Lyn M: Just Lyn M.
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April 27, 2011 10:33 PM
Sorry about the double post. The computer said I had not successfully sent the post.
Posted by: Enkidum
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April 27, 2011 11:39 PM
Can Blattafrax (or anyone who knows, really) point me to a good primer on this? I'm realizing that while I have a semi-reasonable understanding about the "high level" issues involved in evolution, I really know very little about the empirical historical facts of what evolved, why, and how.
Posted by: Michael Hawkins
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April 28, 2011 12:00 AM
I have also come across these dishonest creationists who like to distort good science. In my case, the creationist butchered research about fruit flies. In the particular study there was a straight forward conclusion: genes in sexually reproducing populations do not become fixed in the same way as genes in asexual populations. But to the wee little creationist mind, that meant evolution was somehow false. It's friggin' incredible.
http://forthesakeofscience.com/2010/11/14/butchering-science/
Posted by: Michael Hawkins
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April 28, 2011 12:11 AM
To clarify: The research in question was not mine. My above syntax indicates otherwise, and that was unintentional.
Posted by: Ichthyic
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April 28, 2011 12:22 AM
A lot of people seem to have this all-encompassing fear of science. Its difficult to explain.
It's easier to understand if you look at the arguments various religious pundits have made against "materialism" over the last few hundred years.
they haven't changed their arguments, and it is reflected in their knee-jerk science denialism.
Posted by: TheBlackCat
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April 28, 2011 12:56 AM
Just out of curiosity, does the paper mention when g-protein coupled receptors evolved?
Posted by: Blattafrax
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April 28, 2011 4:19 AM
#71 Enkidum: It's the book I would write, if I had the time or the ability. I don't know of anything off-hand and Amazon isn't much help.
I can however recommend going to http://www.pdb.org every few weeks and looking at their molecule of the month. There's an archive as well. Not much evolution going on, but written for the well educated layman and a huge resource of information on proteins.
#75 TheBlackCat: The paper doesn't mention them, but they would be towards the bottom of the chart. Only metazoa make significant use of them, so with 99% accuracy you could say they were 'born' with metazoa.
But, fungi and plants have them too - in a very limited way. My understanding is that from sequence information alone it isn't possible to determine where the family came from. It looks like they should be related to an archetype GPCR from an ancestral eukaryote. This does make sense when you consider the uses to which higher (sorry) eukayotes use GPCRs. They're mostly for communication from one part of the body to another. Hormone sensors, taste receptors, neurotransmitter receivers, etc. Metazoa presumably co-opted a basic GPCR design for the solution to these problems that only arose with multicellularity. Plants and fungi, with their alternative multicellularity origin found (or had no need for) other solutions to the communication problem. GPCR archetypes still remained and evolved, but failed to find a substantial unoccupied niche they could expand into.
Posted by: masterofhogets
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April 28, 2011 5:29 AM
Hi,
Thanks for a good read - I certainly agree that the findings you mention refute the sort of creationism that claims that there had to be a single, short event that 'birthed' humanity. However, I believe that to claim that God had to rely on such a methodology is almost paramount to blasphemy - a truly omnipotent God could engineer the creation of humanity anyway he wanted - including with multiple seemingly random events over billions and billions of years. I believe Christians who say that this is not consistent with the traditional Genesis account of creation are not reading Genesis for what it is - a poem (with many a poetic device), that is far more concerned with man's relationship with God then it is than with the specific scientific processes of creation.
One only needs to look at Gallileo to see how 'Christains' can misguidedly launch assaults on science.
Posted by: MudPuddles
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April 28, 2011 5:29 AM
Great summary Prof Myers, thank you
Posted by: Thinker
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April 28, 2011 5:39 AM
So, was the decrease in gene births due to an increase in contraception or abortion?
Either way, since creationism tends to correlate with an anti-abortion and anti-contraceptive stance, what do you suppose they intend to do about it? Where will they picket, and who will they target for these unconscionable murders of poor defenseless genes...?
Posted by: Alex, adv. diab.
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April 28, 2011 7:14 AM
@masterofhogets
What's your point? It is a trivial that you can always sneak a God into anything if you make your God subtle enough. 'tis the God of the gaps. That's one thing that makes the God hypothesis so useless.
The fact that you put the 'Christians' in scare quotes indicates that you only consider those people true Christians that do only good. You can define "Christian" any way you want, but that is a very deceptive definition.
Posted by: joed
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April 28, 2011 9:30 AM
Amphiox,
"No, no, no, no, no, no! I'm saying that real humans (not hypothetical fictional ones) don't (not can't) do kind acts without other motivations in addition to kindness. Because real humans never do anything without only a single motivation!"
This says more about you that about humanity, doesn't it!?
Action without motive happens often with all people.
To think a person must have a motive to act with kindness toward another human is like being proud of how humble you are.
Do it sometime: just do something without motive. It may take a bit of practice but when you do it you will notice.
Thanks to the professor for keeping this blog as unruly as it is. Unruly but truly informative, educational and irreverent. Can't beat that combo.
Posted by: rexrexfu
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April 28, 2011 12:06 PM
Back in the Dark Ages of the 20th C., the idea of ancient set points was introduced in geology courses, supported by fossil evidence that all animal body types had appeared in the Cambrian, and that all animals since have been variations on those themes. It's of great interest to read that researchers have extended this consolidation back to bacteria 3 billion y.a.
As for creationists: someday this type of thinking (confused, magical, inability to assign cause and effect) may be classified as a brain disorder. The persistence of irrational belief in the face of fact is certainly maladaptive, but it also is very ancient. The majority of Americans process information irrationally, and therefore magical thinking is accepted as normal. This inability to comprehend physical relationships as described by science is exploited by politicians, religions, corporations, and advertising-marketing. Pervasive magical thinking is exploited to push power agendas, a situation that has been a social staple in our species for thousands of years.
Unfortunately, I think we're dealing with an evolutionary problem within the brain itself.
Posted by: drbunsen
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April 28, 2011 12:58 PM
How can you present an evidence based argument (vaccination efficacy/safety) to people who both misunderstand *and* reject empiricism and reason?
Posted by: call me Rob
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April 29, 2011 1:16 AM
Lurker, first-time poster here. Thanks, PZ, for this blog, and thanks to the Horde for irreverent and enlightening comments.
Please forgive my lack of HTML-fu and insufficient edumacation (undergrad zoology & anthro, 40 years ago).
Two separate comments raised questions for me:
1- Is it accurate to say that multi-cellularity arose independently in fungi, plants, and animals at different times?
2- Re: Tiktalik. If Tiktalik was an evolutionary dead-end, and wasn't the predecessor of tetrapods, then who was? Do we know who was the first tetrapod? Did tetrapod-ness also arise multiple times?
Thanks to anyone who will offer a reply. I promise to re-read Zimmer's "Your Inner Fish".
And thanks for this place & people who are my daily touchstone for sanity and science.
-Rob.
Posted by: Sven DiMilo
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April 29, 2011 1:35 AM
1 - yes.
2 - It is impossible to ever know whether or not a given fossil represents a member of a population that was an ancestor of any living species.
Almost always the answer is likely "not". We have fossils of a vanishingly small proportion of all species that have lived, even for vertebrates.
Posted by: call me Rob
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April 29, 2011 1:36 AM
Ooops! What a rookie mistake.
I meant SHUBIN's "Your Inner Fish". ;)
Posted by: Sven DiMilo
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April 29, 2011 1:40 AM
Zimmer's At the Water's Edge is also good.
If 'tetrapody' evolved multiple times, all the evidence available today suggests that all living tetrapods have a single common tetrapod ancestor (a population). Again, we'll never know for sure what it was, and it probably never fossilized, or if it did we'll never find them.
Posted by: Ichthyic
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April 29, 2011 1:41 AM
If Tiktalik was an evolutionary dead-end, and wasn't the predecessor of tetrapods, then who was?
Think of it this way:
At the time THE common ancestor of all land-dwelling tetrapods evolved, there were probably dozens, if not hundreds, of similar species about (give or take few tens of thousands of years, which is a blip in the time scales we're talking about). The chances that any specific representative of any given species to be fossilized itself is very, very low. Combine these two pieces of information together, and it makes it very unlikely to ever find THE common ancestor you are seeking.
Moreover, all we can do is look at gross morphology, and how it changes in the pieces of the fossil record we do manage to recover. We can't go back and do genetics on these things; there isn't any DNA.
So, we make reasonable inferences about what a common ancestor SHOULD look like, based on what we do know about the genetics and relationships of modern species, and what we have observed as changes within the fossil record. To nail the exact individual would be quite the longshot.
Put another way, it would be like somehow locating THE common ancestor of the Polynesian people, say. You could dig up skeletons until the sun turns cold, and still not be sure you found THE common ancestor of all modern Tahitians, but that there was one at some point is unarguably true, and that we can make inferences about what they probably looked like is also true.
Posted by: call me Rob
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April 29, 2011 1:44 AM
Thank you, Sven.
Posted by: Ichthyic
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April 29, 2011 1:52 AM
However, I believe that to claim that God had to rely on such a methodology is almost paramount to blasphemy - a truly omnipotent God could engineer the creation of humanity anyway he wanted - including with multiple seemingly random events over billions and billions of years.
....and he could have created the world, and everything in it, LAST THURSDAY!
Check the link if you'd like to see what's wrong with your argument.
Posted by: Kel, The Privileged View From Nowhere
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April 29, 2011 1:58 AM
From memory, the paper in question was talking about the sequence of fossils of 'fishapods', and that tiktaalik had characteristics not shared by more tetrapod-like fossils that were shared with more fish-like fossils. That tiktaalik was one of a radiation of 'fishapods' but in all probability not one that was ancestral.
In creationist logic, tiktaalik wasn't a missing link therefore the link is still missing.
Posted by: Ichthyic
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April 29, 2011 2:23 AM
In creationist logic,
why are you intentionally hurting your brain trying to employ THAT?
Posted by: call me Rob
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April 29, 2011 2:23 AM
@ Sven, #87
Thanks for the recommendation re: Zimmer.
The whole process of fossilization fascinates me. Like you say, it seems so unlikely and a bit arbitrary. Paleontology may be more frustration than reward. That makes Shubin's knowledge of geology, and his prediction of where Tiktaalik could be found all the more impressive.
I have a 1/2-inch trilobite fossil purchased in a rock shop. It has inspired me to try to find one on my own. California has Lantham Shales from the Early Cambrian.
http://www.gtlsys.com/Trilobites/Trilobites.html
I'm gonna give it a shot. I have a hammer. ;)
Posted by: Kel, The Privileged View From Nowhere
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April 29, 2011 2:24 AM
The problem with the creationist article that originally quoted the paper was that the creationist writing it didn't have any understanding of what a transitional fossil is meant to be. Hence why a paper talking about other fishapods as good candidates is taken as a weakness in the evolutionary paradigm.
It reminds me of a debate between Massimo Pigliucci and Paul Allen where Allen stated there weren't any transitional fossils - because no fossil met his criteria as being transitional.
Posted by: Kel, The Privileged View From Nowhere
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April 29, 2011 2:30 AM
That should be Robert Allen, not Paul Allen.
Posted by: call me Rob
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April 29, 2011 2:53 AM
@ Kel #91 & #94
Two of my least favorite words are 'missing link'. They have confused many people, including me, obviously.
'Transitional forms' may be a close second.
Markita Lynda, above (#61), said, "branch, then prune".
These are my new three favorite words on this subject.
Posted by: Ichthyic
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April 29, 2011 3:01 AM
It has inspired me to try to find one on my own.
good on ya!
There used to be some good collecting sites around the Simi Valley area, too.
Don't know if they have all been built over now, but worth a quick look.
Also, if you go north a ways, the beach cliffs near Vandenberg AFB will yield excellent fish fossils.
Posted by: call me Rob
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April 29, 2011 3:48 AM
@ Ichthyic, #88
Thank you for reminding me of probabilities, and deep time. Not in the strict mathematical sense, I'll choose to remember this as the Layman's Laws of Large Numbers.
I will try to do my own homework to further my understanding.
You said:
"Put another way, it would be like somehow locating THE common ancestor of the Polynesian people, say. You could dig up skeletons until the sun turns cold, and still not be sure you found THE common ancestor of all modern Tahitians, but that there was one at some point is unarguably true, and that we can make inferences about what they probably looked like is also true."
Thanks, Ichthyic. You have clarified these questions for me. And also helped me tamp down Anthropology Fever when I heard of Australopithecus sediba (4 individuals, lots of remains, complete cranium - wow!).
http://en.wikipedia.org/wiki/Australopithecus_sediba
Apologies to PZ and you all for derailing the Archaean thread with tetrapods, trilobites, and hominids. My bad. Back to lurking and learning.
Posted by: Kel, The Privileged View From Nowhere
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April 29, 2011 4:12 AM
By brain hurts less when I can see the logic in the argument rather than when I don't. There's a certain serenity in being able to see where they are coming from, even if it's from an incredibly stupid place.Posted by: call me Rob
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April 29, 2011 4:53 AM
@ Ichthyic #97,
Thanks for the encouraging words and suggestions re: fossils.
In deference to the Archaean thread, perhaps I'll ask for more details over on The Endless Thread, if you visit there.
Posted by: shjcpr
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April 30, 2011 1:14 AM
No, there is no madness PZ. Even you, in your OP have no choice but to descent into the dreaded design vocabulary pit and declare:
"This represents a period of early exploration and experimentation, when the first crude versions of the genes we use now were formed, tested, discarded if inefficient, and honed if advantageous."
Really PZ, you exhibit that classic Tortucan mentality a contributor on PT talked about. Compartmentalizing opposing concepts.
How well you do it, too; borrow from design advocates as needed, then trash as desired.
You're a keeper, PZ.
Posted by: Uglyhip
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May 1, 2011 12:19 PM
The constant usage of this stupid argument by IDists has helped convinced me that ID isn't even trying to be a science, but rather a philosphy, or perhaps an artistic movement.
I mean, basically, they're saying that scientific findings are invalidated if the language describing them evokes design. Huh? This suggests that "design" isn't supposed to be an explanatory mechanism so much as a sort of feeling that it's all part of a Grand Plan, and PZ's words supposedly betray this feeling.
If the biologists' mental model of what happened is a series of purely conventional, unplanned evolutionary events (as a friend of mine put it, "lots of fucking and lots of death"), then what the hell does it matter if some design-esque words are used as a shorthand? In fact, does this not suggest that it's the language that's limited? I can't really think of a better word than "experiment" to describe the process he's talking about — and, come on, we all know what he's talking about.
If I use "he" as a gender-neutral pronoun in some context, that doesn't mean I think the person must be male, it just means that English doesn't have a decent gender-neutral pronoun. And lots of folks can tell you that deliberately engineering and spreading a new word to replace old ones (whether its a pronoun or scientific term) can be Herculean. It just sort of has to evolve…
Posted by: David Marjanović
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May 18, 2011 5:01 PM
Indeed, we still say "the sun rises" and "the sun sets" even though most of us know full well that it does no such thing.