davegodfrey: Coelacanth (Science)
     Conservapaedia, that bastion of idiocy got its arse handed to it when trying to pick fights with scientists over the Long Term Evolutionary Experiment . This is a multi-million generation breeding experiment involving bacteria, that turned up all sorts of interesting things, including some novel characters of the sort the average creationist claims can't exist. Knowing where to pick its fights its gone after that well-known shaky theory, beloved of Liberals, Relativity.

Andrew Schafly & Co. vs. Physics. Fight! FIght! Fight!

I'm not a physicist, but even I can see most of this is bollocks, and if a physicist can point out to me where I'm going wrong I'd be very grateful.

"The theory of relativity is a mathematical system that allows no exceptions. It is heavily promoted by liberals who like its encouragement of relativism and its tendency to mislead people in how they view the world.[1] Here is a list of 29 counterexamples: any one of them shows that the theory is incorrect."

Now I'm no physicist, but at a cursory glance even I can tell half of this is just crap.
  • The Pioneer anomaly.
  • Anomalies in the locations of spacecraft that have flown by Earth ("flybys").[2]
And how large are these anomalies? I have no idea what caused this- but it could be something to do with the spacecraft itself, unobserved bodies, etc. Its interesting its not been seen with the other probes or indeed planets
  • Increasingly precise measurements of the advance of the perihelion of Mercury show a shift greater than predicted by relativity, well beyond the margin of error.[3]
  • The discontinuity in momentum as velocity approaches "c" for infinitesimal mass, compared to the momentum of light.
  • The logical problem of a force which is applied at a right angle to the velocity of a relativistic mass - does this act on the rest mass or the relativistic mass?
I've no idea. I was never very good at physics. Perhaps the physicists have worked this out? Have you asked them?
  • The observed lack of curvature in overall space.[4]
Space is really, really big. You won't believe how mindbogglingly big it is. I mean, you might think its a long way to the shops, but you can't see the curvature of the Earth at that scale, and that's peanuts compared to space.
  • The universe shortly after its creation, when quantum effects dominated and contradicted Relativity.
We know that QM and relativity don't mesh together. Just because at the very small it doesn't work doesn't mean its not a good theory. it explains lots of things at the very big.
  • The action-at-a-distance of quantum entanglement.[5]
  • The action-at-a-distance by Jesus, described in John 4:46-54.
1. This is another QM vs GR argument. 2. You're taking the word of a book that thinks locusts have four legs against that of mathematics?
  • The failure to discover gravitons, despite wasting hundreds of millions in taxpayer money in searching.
We can't find it therefore it doesn't exist. Gravitons are really had to see. Hell, gravitational waves are really hard to see- you need huge laser beams and supernovae to detect any sign of them. I'm not surprised they're elusive. And aren't gravitons a QM thing anyway? Does relativity require that they exist?
  • The inability of the theory to lead to other insights, contrary to every verified theory of physics.
Well, mainly the things it explains are really big, and really far away. Just because 20th Century physics got obsessed over atoms doesn't mean there aren't things being done with relativity. And are you seriously suggesting that "Not been helpful = Not true" Seriously?
  • The change in mass over time of standard kilograms preserved under ideal conditions.[6]
I think that has rather more to say about what the standard kilogram is made of than it does about black holes, etc, etc.
  • The uniformity in temperature throughout the universe.[7]
Isn't the CMB data a prediction of relativity? Isn't that why this was written?
  • "The snag is that in quantum mechanics, time retains its Newtonian aloofness, providing the stage against which matter dances but never being affected by its presence. These two [QM and Relativity] conceptions of time don’t gel."[8]
Either relativity is wrong or QM is wrong. Which would you rather. (I'm going to ask this question again later).
  • The theory predicts wormholes just as it predicts black holes, but wormholes violate causality and permit absurd time travel.[9]
Just because something is absurd, doesn't mean it isn't true. QM comes up with some ridiculous predictions. And we've seen them happen.
  • The theory predicts natural formation of highly ordered (and thus low entropy) black holes despite the increase in entropy required by the Second Law of Thermodynamics.[10]
2nd law only applies to closed systems. Black holes are not a closed system- stuff falls in, and Hawking Radiation means that stuff falls out. You've tried arguing this one with biologists against evolution. What makes you think physicists will roll over? When you lose to biologists about physics don't pick fights with physicists on the same turf...
  • Data from the PSR B1913+16 increasingly diverge from predictions of the General Theory of Relativity such that, despite a Nobel Prize in Physics being awarded for early work on this pulsar, no data at all have been released about it for over five years.
According to Wikipedia "In 2004, Taylor and Joel M. Weisburg published a new analysis of the experimental data to date, concluding that the 0.2% disparity between the data and the predicted results is due to poorly known galactic constants, and that tighter bounds will be difficult to attain with current knowledge of these figures." So perhaps because there are some things we haven't got nailed down quite so accurately as we'd like (including "g", the gravitational constant) the data doesn't fit the predictions. Predictions which are presumably based on constants which aren't as accurate as we'd like leading to... Predictions that don't quite fit the data perhaps?
  • The lack of useful devices developed based on any insights provided by the theory; no lives have been saved or helped, and the theory has not led to other useful theories and may have interfered with scientific progress.[11] This stands in stark contrast with every verified theory of science.
Really? What about GPS?  And how many peoples lives have been saved by heliocentrism?
  • Relativity requires different values for the inertia of a moving object: in its direction of motion, and perpendicular to that direction. This contradicts the logical principle that the laws of physics are the same in all directions.
  • Relativity requires that anything traveling at the speed of light must have mass zero, so it must have momentum zero. But the laws of electrodynamics require that light have nonzero momentum.
  • Unlike most well-tested fundamental physical theories, the theory of relativity violates conditions of a conservative field. Path independence, for example, is lacking under the theory of relativity, as in the "twin paradox" whereby the age of each twin under the theory is dependent on the path he traveled.[12]
  • The Ehrenfest Paradox: Consider a spinning hoop, where the tangential velocity is near the speed of light. In this case, the circumference (2πR) is length-contracted. However, since R is always perpendicular to the motion, it is not contracted. This leads to an apparent paradox: does the radius of the accelerating hoop equal R, or is it less than R?
I have no idea. But there's all kinds of weird stuff predicted by QM too. Though I'd be interested to see what explanation a physicist has for this. I'm sure there is one.
  • The Twin Paradox: Consider twins who are separated with one traveling at a very high speed such that his "clock" (age) slows down, so that when he returns he has a younger age than the twin; this violates Relativity because both twins should expect the other to be younger, if motion is relative. Einstein himself admitted that this contradicts Relativity.[13]
As I understood it the twin who travels very fast is the one who doesn't age. Time for him has slowed down relative to the other one. I could be wrong, but just because it makes your head hurt to think about it doesn't mean its wrong.
  • Based on Relativity, Einstein predicted in 1905 that clocks at the Earth's equator would be slower than clocks at the North Pole, due to different velocities; in fact, all clocks at sea level measure time at the same rate, and Relativists made new assumptions about the Earth's shape to justify this contradiction of the theory; they also make the implausible claim that relativistic effects from gravitation precisely offset the effects from differences in velocity.[14]
Do they? Do they really? And what shape is the Earth? Precisely?
  • Based on Relativity, Einstein claimed in 1909 that the aether does not exist, but in order to make subatomic physics work right, theorists had to introduce the aether-like concept of the Higgs field, which fills all of space and breaks symmetries.
Even I know that the aether was predicted to exist as something for light to travel through. Its not like the Higgs field. Which might not exist anyway. Not every model of QM needs a Higgs Boson.
  • Minkowski space is predicated on the idea of four-dimensional vectors of which one component is time. However, one of the properties of a vector space is that every vector have an inverse. Time cannot be a vector because it has no inverse.
I find it hard to believe that Minkowski would have got published if he couldn't account for this.
  • It is impossible to perform an experiment to determine whether Einstein's theory of relativity is correct, or the older Lorentz aether theory is correct. Believing one over the other is a matter of faith.
Michelson and Morely would disagree I think.
  • In Genesis 1:6-8, we are told that one of God's first creations was a firmament in the heavens. This likely refers to the creation of the luminiferous aether.
Does it now. Because as I understood it the Israelites believed that the heavesn were a dome and the stars were nailed on. Perhaps thats what the "Firmament" is?
  • Despite a century of wasting billions of dollars in work on the theory, "No one knows how to solve completely the equations of general relativity that describe gravity; they are simply beyond current understanding."[15}
No-one knows how to solve the Navier-Stokes equations. No-one knows if the Riemann Hypothesis is true. No-one knows if super-symmetry is correct. "There's stuff we don't know! It must be wrong!" This is, frankly anti-intellectualism and anti-knowledge at its most sickening.
Comments, especially welcome, as I've cobbled this together after a pint or three, and have, frankly no idea what I'm talking about. Although I have listened to more episodes of "In Our Time", so I'd like to think I had a layman's idea of roughly what these scientist fellows are talking about.
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davegodfrey: Coelacanth (Science)
There's a new paper on the origin of primates. Now I've not looked into primate evolution much (other than criticising the hype around some recent discoveries). But this seemed interesting. In a "Yer what?" way.

Michael Heads has calibrated the origin of the various primate groups to several tectonic events involved in the breakup of Pangaea.

New and Old World Monkeys diverged 120 million years ago when the Atlantic opened. Lemurs diverged from their closest relatives when the Mozambique Channel opened 160 million years ago, and the deepest split in the primate tree, between the haplorhines (monkey, apes, and tarsiers) and strepsirrhines (lemurs and lorises) is 180 million years ago in the Early Jurassic.

This is a problem. The earliest known primate fossil is Purgatorius from the Upper Cretaceous of the USA. (Well maybe. A recent paper in Nature indicates that it isn't a primate but the sister group to placentals as a whole.) Other than that the earliest primates turn up in the Eocene, about 56 million years ago. Molecular divergence times however put the split between primates and their closest living relatives the Dermopterans (the Colugos or "flying lemurs") at about 80 million years.

He is right in pointing out that the previously accepted dates are indeed the minimum dates. Any new fossil discovery could shift them by several million years. Just a week or so ago some tetrapod footprints were found that indicated that tetrapod evolution occurred about 10-20 million years earlier than we thought, creating "ghost lineages", spans of time where no fossils are known, but are expected.

If Heads' model of primate evolution is correct then it creates ghost lineages of 100 million years. This, to me, seems rather excessive. Defending this he points out that several groups do not have a fossil record, yet must be very old, while other modern groups are only known from a few very early fossils (he mentions proscopiid grasshoppers from 110 million years ago). Fair enough, but the molecular dates indicate a ghost lineage of about 25-30 million years from the earliest fossils to the latest divergence times. Increasing this by four times really needs rather more support than he gives it. A new fossil would be enough to make people think.

He is correct in his statements that molecular dates (however they are calibrated) are generally minimum dates, but he repeatedly states that they are "transmogrified" into maximum dates. I can't find any detailed criticism from this paper as to how this is done (do the authors just swap words around? Or are there mathematical tricks that can get you this result?)

Moreover where Heads' paper also falls down is in his refusal to accept that rafting can play a part in evolution and dispersal. It is generally accepted that chameleons originated on Madagascar and then spread. Frogs have made it to Madagascar from Indonesia, and this week a paper was published in Nature showing how ocean currents in the Eocene would have allowed lemurs to raft across the Mozambique Channel, but would prevent them doing so today. He also fails to take into account that the separation of continents is not a simple matter. The North Atlantic began to appear in the Cretaceous, but there were extensive connections between Europe and North America throughout the Eocene, allowing animals to island hop across. I see no reason why South America and Africa would be different.

He doesn't address the issue of why we have a nice transitional sequence of various primate groups in the Eocene, but that isn't necessarily a problem- the footprint paper in Nature gave us the same problem to deal with. However the footprints are evidence for the existence of tetrapods at a particular time period. Heads has not presented any physical evidence to back up his claims, rather he's taken the current distribution of primate groups as evidence that they always lived in these areas, and matched them up with past events. Would he have got the same results if he had used a different group? And if not what does that say about his methods?

Finally, other than ascribing a date of 185 million years to the split at the base of the Archonta (the larger group uniting Primates, Tree Shrews, and Colugos) he says nothing about what this data means for the diversification of other placentals, marsupials or indeed the origin of mammals as a whole. Without running the mathematics I can't help get the feeling that were this paper correct it would push the origin of mammals somewhere into the Permian. Which seems, shall we say, extremely unlikely given the fossil record we have there.

As they say, extraordinary claims require extraordinary evidence.

Michael Heads: Evolution and biogeography of primates: a new model based on molecular phylogenetics, vicariance and plate tectonics, Zoologica Scripta, Published Online: Nov 10 2009 4:44AM DOI: 10.1111/j.1463-6409.2009.00411.


J. R. Wible, G. W. Rougier, M. J. Novacek & R. J. Asher: Cretaceous eutherians and Laurasian origin for placental mammals near the K/T boundary, Nature 447, 1003 - 1006 (21 June 2007)
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davegodfrey: Coelacanth (Science)
Does anyone have access to November' 2009's Zoologica Scripta? I'd like a copy of the following paper please.

Michael Heads. Evolution and biogeography of primates: a new model based on molecular phylogenetics, vicariance and plate tectonics. Zoologica Scripta, 2009.

It suggests that lemurs and lorises diverged from the new and old-world monkeys about 180 million years ago, (the early Jurassic). I'd like to post a criticism of it, but I'd rather wait until I've read the paper. After all, he might have included some important data that hasn't made it into the press reports that explains why placentals should be found in the Permian, or that he's produced a ghost lineage based on no fossil evidence whatsoever that's about 100 million years long. Like I say. I don't want to be prejudiced.
davegodfrey: Marvin: ...and me with a terrible pain in all the diodes down my left hand side... (Marvin)
OK. I admit it. I didn't vote. I had my ballot way in advance, I have a postal vote as I'm registered with my parents, rather than where I live at the moment. I'd even voted, put everything in the envelope, and had it in my bag ready to post. And I totally failed to actually send the damn thing off.

And then I discovered that If I had voted I'd probably have voted against my principles anyway. We had four candidates in Dartford East in the council elections, the Conservatives won it (unsurprisingly) but the Lib Dems (who I voted for in this one) were beaten into fourth place by the "English Democrats". Turns out the English Democrats sound an awful lot like UKIP, and want to leave the EU, end "mass immigration" and "those laws promoting political correctness repealed." It seems they "want English freedoms and values, not multiculturalism." I wonder how many of them drink lager and eat curry. Hmm. They got about twice as many votes as the Lib Dems.

Damn.

And now for the European Elections. Here I would have voted Green. And then the day before the election I discovered their stance on Embryonic Stem Cell research. As
Sciencepunk reports:

The Green Party believes that experiments on human embryos could have unforeseen outcomes harmful both to individuals and to society. We would work for an immediate international ban on all cloning and genetic manipulation of embryos, whether for research, therapeutic or reproductive purposes. We do think that the use of 'adult' (or 'mature') stem-cells has promise for both research and therapeutic purposes and does not involve the same risks and ethical issues as embryonic stem-calls. The Green Party would work to allow the use across the EU of adult stem-cells, subject to the precautionary principle.

It does not mention exactly what the risks are. (are they really going to be any different from those involved in adult stem cells. Really? Digging a bit further into their policies on science I'm finding more to disturb me.

HolfordWatch has an excellent summary of their health policies, which range from a rather detailed policy on banning mercury fillings (but rather less on any other aspect of modern dentistry), and the very worrying support for "complementary" medicine, including homeopathy, etc- most importantly their proposal that they will:

...encourage the development of a wider and more relevant range of research techniques, including methods appropriate to the assessment of complementary therapies.

As Ben Goldacre, HolfordWatch and others repeatedly demonstrate the standard scientific toolkit works very well at evaluating the claims made by homeopaths, nutritionists, and others. Unfortunately for them they are less than complementary about the efficacy of the proposed treatments. Are the Green Party really this anti-science? At first their policy on Genetic Modification seems reasonable.

ST362 The Green Party accepts that certain aspects of genetic engineering may be benign and may lead to enhanced quality of life, but feels that there is an urgent need for informed public debate on the issues raised because of the economic, environmental and social control aspects of this technology

ST363 Pending research into the effects of the release of genetically engineered organisms into the environment, the Green Party seeks a moratorium on such releases through agreement between industry, research establishments and government, as well as a ban on importation of such organisms into the UK. (see AR410)

AR410 Patents will not be granted on any animal and strict controls will be introduced to prevent genetic manipulation for profit or curiosity

Fair enough you'd think- the public understanding of science is something I want to see vastly increased, I too am concerned about Monsanto and co patenting crops, and using terminator genes to force farmers to keep buying their seeds. Similarly most GM that's actually been used in agriculture merely allows you to use more pesticides, rather than increasing yield, drought resistance, or something really helpful there.

However the key wording is this: a ban on importation of such organisms into the UK.

Gimpy is a life sciences researcher who performs genetic modification on organisms for research purposes. Some of you may know that I was prescribed Human Growth Hormone while I was a teenager. This was not obtained from cadavers, but from GM bacteria. Its where diabetics get their insulin, and is going to be a source of plenty of other drugs- after all bacteria are cheap to grow, and can produce the chemicals in much larger quantities than the original organism usually does. Science is an international, collaborative effort. Scientists regularly send each other samples of the organisms they're working on, and Gimpy is naturally concerned that ST363 and AR410 sound like the Green Party's policy could have real problems for scientists if they gained a position of power.

At least when pressed by Gimpy for clarification a (unnamed) Green Party member stated that:

I must admit I don’t know what the purpose of that last part of ST363 is, since clearly there could be importation for research where there is no potential environmental problem, and I can’t see that there is necessarily a problem in the circumstances you describe.

We review our policies from time to time, and maybe we need to take a look at this one!

Damn straight! I think you do. Is that a reason not to vote for them? I don't honestly know, certainly in Europe they've done much to get climate change onto the agenda, something that I'm worried will suffer with UKIP's rise to prominence and their avowedly Anti-Global Warming stance.

I rather like (at least in principle) the Green's policy of allowing all members to propose policy, which then gets voted on, leading to such things as a clearly defined policy on mercury fillings in teeth, but somewhat more ambiguous statements on genetic research that they admit they don't know the intention of worry me.
davegodfrey: Flying Spaghetti Monster : Touched by his noodly appendage (FSM)


"Charles Darwin wasn't a scientist but a theologian"

Darwin did indeed study theology- but then so everyone who didn't take medicine. At the time Cambridge offered two degrees- Medicine or Divinity. And aside from natural selection Darwin wrote one of the definitive works on barnacles and worked out how coral reefs formed. That makes him a scientist, regardless of what he read at university. By this reasoning Margaret Thatcher is a chemist. Oh, and Darwin lost his faith after he came up with Natural Selection, not before.

"No transitional forms"

Pakicetus, Ambulocetus, Rhodocetus, Basilosaurus, Dorudon, and just today Maiacetus. And that's just the whales I can think of off the top of my head.

"The cell is one of the simplest units of living matter"

Life spent the first 2 billion years as bacteria. It took a very long time to get that complex. Oh and stop it with the "Chance and time" bollocks. Evolution IS NOT A RANDOM PROCESS!!" Mutation is random. Selection is non-random.

"irreducible complexity"

Oh crap she's discussing Behe's flagella stuff. The flagella is developed from the Type 3 Excretory system present in a variety of other bacteria. Has she never heard of the phrase "pulling yourself up by your bootlaces"? Because that's how evolution works.

"Wake up and acknowledge God created you"

Hail the All-Father! Oh sorry not the god you were referring to? How about Queztzalcoatl? Not him either? Bacchus? Tiamat? Ra? Crom? Azathoth? Geoff?

The video comes from the "Passion for Christ Movement". Note the Ex-Atheist T-shirt she's wearing. Coupling the standard creationist nonsense with their "Ex-Homosexual" T-shirts,and the "your body is something to be ashamed of" cant tells you everything you need to know about these people I think.

H/T to Pharyngula and Feministing
davegodfrey: South Park Me. (Default)
Was really very good, but it did confirm my personal dislike for Ricky Gervais. However the host, Robin Ince was very, very good, with his Hannah-Barbera Feynman impressions, and humorous rants about Anne Coulter, Stephen Green and all the other people who provide a reason for the "New Atheists" to be so vocal. Plus he gave a shout-out to Tycho Brahe. Who doesn't get talked about nearly often enough at comedy gigs.

There were a couple of acts that didn't quite work for me. Mostly it was the musical numbers. Which I'm sure were a matter of personal taste. I'm not really sure that the one-man Beach Boys parody quite fitted.

The Carl Sagan snippets were very well chosen. I never watched Cosmos when I was a child. I don't think they repeated it much in the 1980s, unlike the ubiquitous deity that is Sir David A. But on the basis of those few minutes I can understand why he was so popular with so many people. (And then the Mystery Fax Machine Orchestra played a very silly version of Thus Sprach Zarathustra).

Simon Singh was good, and it was nice to hear his Katie Melua rewrite- as sung by the lass herself. I remember hearing it on the Today programme a few years back.

I can understand why Dawkins chose the pieces he did, and it reminded me that I still haven't got a copy of Unweaving the Rainbow. Though if he'd spent the entire time talking about Fig Wasps that would have been equally enjoyable.

Stewart Lee was very good too. I will never hear the "dance as ancient as time" cliche in quite the same way.

Natalie Haynes was rather funny, and I shall have to look out for her work in future.

Ben Goldacre's polemic was fantastic. His columns are always worth reading, and he brings the same mix of wry humour and outrage at the actions of people like Matthias Rath to his spoken word stuff too, and provided a reminder that pseudoscience is not harmless.

Tim Minchin rounded off the evening with a brilliant beat poem. Someone else I shall have to look out for in future.

Sadly I couldn't find someone to take up the spare ticket I ended up having. But at least this time I remembered I was supposed to be at a gig. ;)
davegodfrey: South Park Me. (Default)


Who does this woman have for a science advisor? Ken Hovind? I knew she was in favour of ID, I've heard the McCain rhetoric about the $3m "overhead projector" for a planetarium. Properly funding education for people with special needs is a very worthy aim. I don't doubt that the some of the "earmarked" pet projects aren't worth spending money on. But they've made themselves look very silly by picking on the science ones.

But really? This is insane. This woman has a son with Down's Syndrome. Drosophila melanogaster is a model organism. Basic research on this animal has taught us an awful lot about the genetic and developmental basis for thousands of conditions affecting millions of people. Many of them with the special needs that Palin is so keen on helping.

Comments on Pharyngula claim that the research she is criticising is on the Olive Fruit Fly (not D. melanogaster), which is now a major pest in California. It is native to Europe, so doing the research there makes perfect sense. Now one could make arguments about whether the amount of money spent is worth it given the size of the olive growing industry, and distinguishing this research from that research. (Is spending $211,000 on an industry worth $59.4m in 2006 worth it? Its a criticism one could make. But not the one she did.) Of course what happens if the fly evolves and changes host? You might want to have done some research on the animal to understand its ecology to see how or if this might happen, and how to control the thing if it does.

Of course Palin and McCain are harping on about helping small businesses. I'd have thought that $211,000 to control a pest that can wipe out the that year's souce of revenue of just such a small business might actually be of more benefit than the tax cuts.

I don't doubt that there are pet projects that probably don't deserve government funding, but renovating the Adler Planetarium (which needs a new "overhead projector" because its 40 years old, and the company that made the old one can't service it any more) sounds like the sort of thing which makes the government look good. Its a nice project that will do much to inspire children across the wider area. And if the new kit lasts as long as the old one its only $75,000 a year. And the government aren't going to be paying for the whole thing anyway are they?

Besides aren't kids with special needs allowed to be interested in science? I don't know anything about the Adler's education programme, but I would be very surprised if there was no provision for children (and adults) with all kinds of disabilities.
davegodfrey: South Park Me. (Dave Godfrey)
Andrew Schlafly (Phyllis Schlafly's son) recently founded Conservap(a)edia. It is (as you might guess) an alternative to wikipedia because of the "liberal bias" it apparently has.

Dr. Richard Lenski is running the Long Term Evolutionary Experiment (LTEE). For the past 20 years he has been growing a culture of E. coli in a medium where glucose is  the limiting growth factor. Lenski has twelve evolving populations , and every 500 generations samples are taken and frozen giving them a "fossil record" palaeontologists would sell their mothers to have. The aims of the LTEE is to observe patterns of contingency and convergence. So far the bacteria have been converging- they're considerably bigger than they used to be, and show a wide variety of other adaptations that have appeared in parallel. However...

With his collaborators, Zachary Blount and Christina Borland, Lenski has discovered that E. coli in one of the populations has evolved the ability to take up and metabolise citrate (known as Cit+). The citrate is in the medium to help the bacteria take up iron, but never normally enters the cell. Importantly E. coli can't eat citrate in aerobic conditions- its one of the defining characteristics of E.coli. (It seems there have been two other reports of Cit+ in E. coli and they've both come from swapping plasmids with other bacteria). The bacteria in the experiment lack plasmids, and only reproduce asexually. The scientists used their fossil record to investigate the process of Cit+ evolution, ruling out plasmids and contamination, and then tracking the process of Cit+ evolution. It seems there are at least 3 mutations involved, they didn't happen all at once, the earliest bacteria able to survive on citrate did so very poorly, and research remains to see what exactly is going on at the genetic level.

The paper is available online (pdf). You can also read abstracts and some pdfs from all the publications to come out of the LTEE.

The fact that one population is now significantly different from the others makes it very interesting to watch, because they've got a really visible, and important example of contingency. So lots to look forward to, and plenty more research to do. Carl Zimmer's been keeping a good blog on this, and Zachary was kind enough to turn up in the comments, offered to answer questions, and point people to other papers from the LTEE. Unfortunately a creationist turned up who didn't understand the meaning of the word "goal", so the whole thing turned into a car-crash. Zachary should have a guest post up there soon, dealing with some of the questions. (Excuse me I appear to be getting teary-eyed at a scientist engaging with the public- its so beautiful when it happens.)

Anyway, why did I mention Mr Schlafly? Well over at Conservapedia he wants Lenski to provide him with 20 years worth of data. He has it seems "skimmed" the paper and quoting PNAS's rules thinks he can demand this. Lenski politely points out that 1. the data is in the paper, and 2. he isn't saying what Schlafly thinks he's saying. This isn't enough for Schlafly, who complains that he must have access because they're taxpayer funded, and they sometimes say "data not shown". Lenski replies again, and I can't summarise it other than to say that Schlafly gets his arse handed to him on a plate. There are some beautiful quotes which I shall share, but you should read the exchange, at RationalWiki.

"If you have not even read the original paper, how do you have any basis of understanding from which to question, much less criticize, the data that are presented therein?"
"Am I or the reporter for NewScientist somehow responsible for the confusion that reflects your own laziness and apparent inability to distinguish between a scientific paper, a news article, and a confused summary posted by an acolyte on your own website?"
"But perhaps because you did not bother even to read our paper, or perhaps because you aren’t very bright, you seem not to understand that we have the actual, living bacteria that exhibit the properties reported in our paper, including both the ancestral strain used to start this long-term experiment and its evolved citrate-using descendants."

And for my American friends, an explanation of the differences between cricket and baseball. (It certainly explains why I understand cricket better than baseball.)

(Via PharyngulaBad Science, and pretty much everybody else by now.)
davegodfrey: Coelacanth (Science)
Some of you may have seen this paper at PLoS ONE. Its a rather nifty piece of work by Darren Naish and Mark Witton (who's very nice drawings accompany the article itself, and the various newspaper reports.)

Basically a group of pterosaurs called Azdarchids have always been a bit of a problem for palaeontologists working out their lifestyle. They're huge, with 10m wingspans, 2-3m jaws, and "it could look a giraffe in the eye". Originally suggested to be variously scavengers, "dip feeders" (like albatrosses), and mud probers, but they don't have the right sort of beak for any of those. Along with every other bloody pterosaur they've been suggested as a "skim feeder"- but no pterosaur is nearly as specialised as Rhychops the skimmer.

Naish and Witton therefore reconstruct them as stork-like predators. The fossils are mostly found in terrestrial deposits, and their footprints indicate their feet aren't adapted for wading (another popular hypothesis)

Yet again coverage is varied. The best place is of course the paper itself, freely avaliable online. Or you can read Darren's blog about it. I wouldn't bother too much about the rest of the media though. 

  
ETA: The Economist, another short article, and nothing wrong here either. States the research showed that they "were more like giant storks. Rather than skimming the sea, they plucked their prey from the ground." Better than the Sun article, but frankly not that much. Again, shorter seems to be better.
davegodfrey: Marvin: ...and me with a terrible pain in all the diodes down my left hand side... (Marvin)
Imagine you've been given millions to make your film. It involves aliens. These aliens will be seen as non-moving prop remains, and live ones will be rendered in CGI. You therefore have free rein to make them look as weird as your imagination allows.

So why do they always make them look like humans with funny shaped heads. WHY GODSDAMMIT!?!? I'm not really talking about Who or Trek here, where you've got a relatively limited budget, rather more limited time, and its really the characters rather than their appearance that is the big draw. But even then Who made an effort with Rutans or the Nestene.

The skeletons are almost always tetrapod- virtually always with the pentadactyl limb. You can usually identify these things as probably mammalian, because they lack abdominal ribs. The rest of the skeleton could pass for human most of the time. The most they ever do is make the eyes bigger and stretch out the back of the skull. Even if you're going to stick with the vertebrate bauplan humans aren't that interesting. There are snakes that can give you a bite with their mouths closed, legless amphibians with sensory tentacles and protrusable eyes, and have you ever seen a baleen whale's skull? This is before we get out of the tetrapods. If you allow yourself fishes you've got all kinds of weirdness to play with. Add invertebrates to the mix and you'll get things that wouldn't be out of place in a Lovecraft fantasy. What's more because people are unfamiliar with them they'll be even more alien than some chap in green make-up with a fake eye in the middle of his forehead.

As long as you can make something like this work under gravity I don't care. Let your imagination run away with itself. Or leave their appearances hinted at, but no more. Let me conjure up bizarre flights of evolutionary fantasy if you don't have the vision to merely tweak a primate.
davegodfrey: Coelacanth (Science)

Professor PZ Myers blogs at Pharyngula (***Warning: This website contains profanity and may be offensive to some listeners. KKMS politely warn us. It'll be the cephalopods won't it?) .
He's a fairly strident atheist, but more importantly he's an evolutionary biologist working on zebrafish development. He also likes fossils, and is generally fascinated by the natural world.

Dr Geoffrey Simmons is an honorary fellow of the Discovery Institute. (***Warning: This website contains idiocy and may be is offensive to anyone who knows about science.) 
He is a doctor with an interest in disaster medicine and management.

Both were invited on the Jeff and Lee Christian Talk Show, to discuss the evidence for ID and evolution. Simmons didn't like this idea and so demanded that the title be changed to "Is Darwinism a fact or faith issue" at the last minute. (Which was nice of him).

What follows is 40 minutes of creationist trouncing. Its just glorious. Simmons brings up Indohyus and claims this is the only whale ancestor. PZ responds with Pakicetus and Rhodocetus, "but theyz have nao bloholz, and they finz iz funnie?". Simmons it seems has only read a single article in Scientific American about this, and hasn't heard of any of the other whale fossils.

Rapidly backing off he then tries "Groth ov brainz iz complicated. Muzt bin dizignd!". Like I said PZ is a developmental biologist, working on fish brains, teaching college students neuroscience.As he said: "I'm afraid you've stepped right into my field there with that question".

You can't listen to the calls they took afterwards, (someone may make a version covering them too) but the one I heard was entertaining. A chap called in expressing the view that:
"evolution gives us easy justification for passing what we learn about drugs when used on animals to predict how they'll work on people... [and pressing them] on whether we should scrap that belief if we reject evolution."
The hosts response? Affter rambling about taking a "more holistic approach", and "having a doctor who relies on God's guidance" they ask:
"Do you believe there's any use or purpose for theology?"
"As someone who has my bachelor's in theology, I hope so".

PZ's take on this beforejust before and mopping up afterwards.

The Discovery Institute's take on it is here. (archived here 'cos they deleted it).

Download the MP3 here. if the podcast isn't up yet. You know you want to!

Oh, and I want "Your ignorance is not evidence" on a T-Shirt.

davegodfrey: Coelacanth (Science)
"Dr" Gillian McKeith, aka "That Awful Poo Lady" is no longer permitted to use the title "Dr" in any of her advertising. I personally think she shouldn't be allowed to use the title "Dr" in her name, as she got it from a non-accredited degree mill on the basis of a 46 page pamphlet on the supposed health benefits of "blue-green algae". Its also an insult to the people I know who slogged their guts out to produce backbreaking 1,000+ page tomes. (Maths PhDs are probably much shorter, but 20 pages of solid equations would require just as much work).


Its not just the stupid science and the bullying that get to me. She shares something in common with an awful lot of other "woo merchants". The attitude of blaming the victim. While doing something about poor diet and lack of exercise will help you, I don't think it accounts for the disparity in life expectancy between rich and poor. Goldacre's article cites the difference in average lifespan between someone who lives in Hampstead (78) and Kentish Town (70). I've read similar stats in a Steve Jones book (using -iirc- the District line for comparison). For practicioners of alternative "medicine" if their hyperoxygenated water or chelation therapy or the laying on of hands doesn't work its because the patient didn't believe enough, or didn't have the right attitude. It couldn't possibly be because the "cure" can't work now could it? Blaming the victim makes good TV, pointing out the uncomfortable truth about the difference between rich and poor that influences such things as diet choice makes politicians uncomfortable and can't be allowed. Its not just health, this attitude permeates many other areas of political debate. I'm sure you can think of some.
davegodfrey: South Park Me. (Dave Godfrey)

A Libyan court has sentenced five Bulgarian nurses and a Palestinian doctor to death for "knowingly infecting 426 children with AIDS. The problem? There is absolutely no evidence they were responsible. Initially found guilty and sentenced to death in 2004 the supreme court quashed the verdict and ordered a retrial. Surprise, surprise they got the same result.

An article in Nature demonstrated that the strain of HIV involved was prevalent in the area, and that the outbreak was probably began before the accused medics arrived at the hospital. This appears to have come too late to help the case. Confessions under torture appear to have been made, though the police officers involved have been acquitted. Many of the infected children also had Hepatitis B and/or C, indicating that poor hygiene was a far more likely cause that deliberate infection. Witness testimony was ignored (including statements by the guy who discovered HIV).

The president of an organisation representing the victims made a statement claiming that the children had been infected with a "genetically engineered" virus under the supervision of Western intelligence agencies.

The case has been appealed against and may go to the Libyan Supreme Court.

Watch This Space as they say.

????

Oct. 18th, 2006 08:40 pm
davegodfrey: Coelacanth (Science)
Humanity may split into two species... and monkeys may fly out of my butt.

Some twit at the London School of Economics- that well known science establishment- has stolen the plot of the Time Machine for "Bravo TV" of all people as his latest science project.

Apparantly in the near future (3000AD) humans will be 6-7 feet tall and live to 120. Everyone will look like supermodels and pornstars. Men will have bigger penises, square jaws and sing baritone. Women will have glossy hair, smooth hairless skin and pert breasts.

That's nice, but evolution doesn't work that quickly. If its going to happen in the next 1000 years then everyone under 5'5 is going to have to stop breeding. Now. Besides height has a lot to do with environment (though in my case f*cked up growth hormone and short parents was more important). 

Then because we rely on technology to solve our problems our immune systems will shut down and genes that allow cancer (that gets treated) can be passed on. Riiight.

Part of this is correct- late acting genes that contribute to the carrier's death are common (Huntingdon's disease, genetic components of cancer, etc). However I think its more likely that in the intervening centuries these will be removed from the gene pool via designer babies, etc. Similarly if everyone breeds with everone else racial differences will be lessened.

From this persistence of crappy genes we get the "short, squat genetic underclass". Are people going to refuse to mate with each other Gattaca-style because of defective genes? If people are going to be this choosy about their mates then any gene that makes you shorter, squatter and uglier won't spread very far.

And so we end up with the Eloi and Morlocks. Don't forget, the Morlocks were eating the Eloi and running the whole shebang till that pesky Victorian gent turned up.

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The Evil Atheist Your Mother Warned You About

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