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if it [this warming] is maintained for a century the Earth's temperature will approach that of the middle Pliocene (2.75 million years ago), when the world was about 2C warmer than today and sea level was at least 25 m higher.

Taken from a paper you can find here

If you think that a 25 meter increase in the sea level will be cheap to adapt to, you are not probably one of the millions living in the coast.

Adaptation is cheap, while prevention is hideously expensive? I think that the underlying feelings for many people speaking like that are in the line of "Adaptation can be left to the next generation while prevention would mean some costs for us NOW". How generous.

Do you have any idea how many times the old "start with a colony of clones that lack antibiotic resistence and watch antibiotic resistence emerge" experiment has been done?

I can't seem to find these papers. I found this one:

http://www.pnas.org/cgi/content/full/100/17/9658?m axtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=g enomic+evolution+antibiotic&searchid=1138477885820 _2558&FIRSTINDEX=0&journalcode=pnas

But it seems to say that the antibiotic resistance was already there, only not being selected for.

I said:

The "mutation" you refer to is not necessarily the generation of new genetic code, but can very easily be the expression of existing code that wasn't active before.

You said:

That sort of implies that you had done some actual reading about the mutations I referred to. It's fairly clear that you haven't and you're dismissing the idea out of hand because you think that they could "very easily be" something else. So, the question again is, did you read the relevant material to see if they discussed the possibility, or are you assuming that you're the only person who had considered it?

I direct your attention to this paper http://www.pnas.org/cgi/content/full/96/7/3807 , a study of 10,000 generations of E.coli in which Papadopoulos, et al, conclude:

"We have not yet determined the molecular events responsible for the genomic changes detected in our study. However, three lines of evidence suggest that they are mostly due to IS transposition and other types of chromosomal rearrangement."

Also:

"Finally, we observed significant changes in the copy number of certain IS elements (Table 2); these changes are most easily explained by transposition and deletion events that produce gains and losses of copies, respectively."

I'd say that those conclusions support my point. Yes, these are forms of mutation, but they are not generating new, novel functions, they are just copying and modifying existing functions. Microevolution, in other words. That's what I was trying to point out.

This is an improvement on a known technique. The abstract is as over-reaching as the press release (the linked article).

  I'm not a crystallographer, but I work in a lab group that has many crystalographers in it.

  It's been known for some time that you can use a variety of materials - including things with porous surfaces, which is what is used here - to assist the process of crystallization. Crystalization is difficult and, frankly, rather unscientific - you take the protein you want to crystallize, and you try different techniques and tricks (of which porous nucleants are an example) until you can get it to work.

  So, okay, it would be a "holy grail" if you could find one technique that would let you crystallize most things without going through all that trouble.

  However, based on only seven examples (Subscribers only, I'm afraid.), you absolutely cannot conclude that this is a universal nucleant - based on the similarity among the seven examples, I'd be very surprised if it were; even if it were a universal nucleant, nucleation does not always guarantee usable crystals.

  Those caveats aside, it does look like a useful advance.

This is an improvement on a known technique. The abstract is as over-reaching as the press release (the linked article).

  I'm not a crystallographer, but I work in a lab group that has many crystalographers in it.

  It's been known for some time that you can use a variety of materials - including things with porous surfaces, which is what is used here - to assist the process of crystallization. Crystalization is difficult and, frankly, rather unscientific - you take the protein you want to crystallize, and you try different techniques and tricks (of which porous nucleants are an example) until you can get it to work.

  So, okay, it would be a "holy grail" if you could find one technique that would let you crystallize most things without going through all that trouble.

  However, based on only seven examples (Subscribers only, I'm afraid.), you absolutely cannot conclude that this is a universal nucleant - based on the similarity among the seven examples, I'd be very surprised if it were; even if it were a universal nucleant, nucleation does not always guarantee usable crystals.

  Those caveats aside, it does look like a useful advance.

The abstract is available and the whole article is available for purchase for those interested.

It says: That it was presented in "Proceedings of the National Academy of Sciences" (that's the November 28 issue). That leads us to the Abstract for the paper, where you have to BUY the paper, you know peer review costs lots of money.

In the Cal tech press release, you can see that the researches are Michael H. Dickinson, Esther M. and Abe M. Zarem, and Douglas L. Altshuler. They all work in the Dickinson Lab which has some cool equipment for researching flight of insects.

Although I do agree with you in that the research is wonderful without the mention of the controversial 'theory', it is the prerogative of the researcher (Douglas Altshuler) to talk about ID if he wishes. Please note that the "pissed-off researcher" is the scientist that did the research. Actually, he's the first author on the paper, which probably means he did most of the work (while Dickinson was his research advisor). He may have been extra-motivated to do this particular research in order to 'stick it' to the ID'ers. If that's the case, he deserves his podium. Research is a form of truth. Truth cannot be cheapened no matter how politicized the discussion is. My own personal opinion is that this research is extra interesting since ID'ers do talk about the bee-flying phenomenon as an example of the wonder of God. With that in mind, this experiment and its connection to ID is a very dangerous precedent. Are we playing into the hands of ID'ers? Are we now obligated to prove scientific logic for every question ID 'theory' poses? That's going to take a while... Even so, why is it so bad if its the ranting of a "pissed-off researcher" or a "reporter with an agenda"? Is the science/research any less truthful? -j

The published work is here, which explains that the gene affected is myostatin.

Myostatin, aka GDF-8, is only expressed in skeletal muscle and not cardiac or smooth muscle: "There are several TGFb s subtypes which are based on their related structure. One such member is called growth and differentiation factors (GDF) and specifically regulates growth and differentiation. GDF-8, also called myostatin, is the skeletal muscle protein associated with the double muscling in mice and cattle."

Full journal article (PDF)

How has Slashdot moderation become so broken?

Photochemical Generation of Carbon Monoxide and Hydrogen by Reduction of Carbon Dioxide and Water under Visible Light Irradiation

Or why not do the same with evolution? So why do you answer a question with a question? By doing so you dodge the question of why not prove something before believing in it. Because if you do it backwards you will end up believing whatever you cultural heritage suggests.

As far as your question goes - Ues starting by questioning evolution or old earth assumptiong is recommended. And yes, there is a preponderance of evidence to support evolution and old earth. Again, as in angular unconformities, I prefer the simple examples as evidence versus detailed technical arguements. For example, any physical geologic separation of life forms such as a continent, island or mountain range are attendent with variations of life forms and formation of related species. Look at Madagascar, Australia, Gelapagos islands, or Sierra Nevada mountains. Predicted and actually required by evolution but not predicted or even suggested by creationism.

Doctor Hovind has not made _any_ contributions to science or geology. He has no formation training in science. If Hovind has been dishonest in his credentials, question everything he has to say. Beware of the individual who is "dishonest for god".

Unconformities do not typically involve bending of rock. Which makes it more difficult to deal with on a short time frame. Many unconformities, such as ones at the bottom of the Grand Canyon, do not have significant bending - so to have them tilted as "soft muds" with no distortions would be improbable if not impossible. To have large sections of the earth move in parallel requires lithification or solidification before tilting and uplift and erosion. A few nice examples:

Example 1 Example 2 Example 3 Example 4

BTW bending of solid rock is not difficult at high hydrostatic pressures and temperatures.

Again, I haven't read a lot of actual science studies on geology I don't think you necessarily need to. You need a little scepticism, discernment and common sense to appreciate angular unconformities and other geological structures. For example, in this photo photo which deposition layer represents the flood. These are gravel layers separted by lava flows. Presumptions are not required to understand the earth is old and tortured.

BTW you last arguemenst sounds a lot like relativism. Truth does not care about your relative view point.

It's happening, though you have to start with more fundamental processes and work your way up. Basically if you can make hydrogen and carbon monoxide, you can make anything.

I noticed in some of your other posts you talk of origins. Evolution is no more about the origins of life than chemistry is about the origins of the elements.

Right, and if you read my posts in this thread carefully, you'll see that I confine my discussion to the application of evolution to the origins of life, to which, as you state, it does not apply. Darwin was very much correct when he noted, "Gosh, it sure is easy to breed animals for our own purposes." However, since this discussion is about whether it is reasonable to assert that evolution, or anything else, was the origin of life, I think I'm missing your point.

If you're up for an interesting study by an evolutionary biologist which indicates that the time required for change due to environmental stimuli grows exponentially the farther one drifts from the original "ideal," (such as would suggest that evolution as origin is mathematically problematic,) try:

http://www.pnas.org/cgi/content/full/98/16/9157

Internal memos from Philip Morris from April 1980 indicate that the tobacco companies have been fully aware of radioactivity in cigarettes for over two decades. They also knew of ways of eliminating the radioactivity, but wrote them off as a "valid but expensive point":

That phosphate fertilizer (specifically superphosphate fertilizer) contains natural radioactivity is a well established fact.

Natural uranium accumulates in the phosphate rock and has been shown to substitute for calcium in the rock structure. Uranium and its daughters are thus carried through the mining and manufacturing process and appear in the commercial product. Soils to which these products are applied show an increase in radioactivity over that naturally present and this increase is a function of the rate of application and the number of years that the fertilizers have been used.

M. E. Counts has shown that the specific [radio]activity [...] increases as the particle size of the superphosphate fertilizer decreases. Thus the smaller particles, which would be more likely to be made airborne by normal farming practices, would be expected to settle out on the tobacco leaves during the growing season and/or be more readily taken up by the plant root system.

210Pb and 210Po are present in tobacco and smoke. The Martell "Hot Particle Theory" has been addressed in the past and has apparently lost popularity in the scientific community (lack of recent publicity in this field). For -particles from 210Po to be the cause of lung cancers is unlikely due to the amount of radioactivity of a particular energy necessary for induction Evidence to date, however, does not allow one to state that this is an impossibility. (Ed: and of course, more recent evidence says just the opposite)

The recommendation of using ammonium phosphate instead of calcium phosphate as fertilizer is probably a valid but expensive point. What Martell appears to be suggesting is the purification of phosphate rock to obtain P2O5 or H3PO4 free of calcium (uranium and daughters) and inert materials. Preparation of ammonium phosphate for fertilizer would then yield a product greatly reduced in or free of the natural radioactivity present in the parent phosphate rock.

Furthermore, switching to indirect fire curing would eliminate virtually all of another carcinogen, nitrosamine, from cigarettes. Nitrosamine was previously found in BEER thanks to direct fire curing of barley. Switching to indirect fire curing of barley reduced nitrosamine in beer to indetectable levels. Yet Philip Morris makes Marlboros, cigarettes with more nitrosamine than any others in the world.

Yes, believe what Philip Morris says, because if you realized there could be a safe cigarette, it would cost them a lot of money...

Here's two simple manufacturing changes they could make which would eliminate the two most potent carcinogens from cigarettes. But I guess it's just cheaper for Philip Morris to kill their customers.

...But the gene only stops HIV type 1. The delta 32 gene mutation would not prevent infection from HIV type 2.

From this journal:

"Human immunodeficiency virus (HIV) type 2, the second AIDS-associated human retrovirus, differs from HIV-1 in its natural history, infectivity, and pathogenicity, as well as in details of its genomic structure and molecular behavior."

Type 2 is the predominant strain of the virus in Africa, so knowledge of the delta 32 mutation will have little effect on the spread of the virus in this epidemic.

However, this discovery can still potentially lead to a vaccination/cure for HIV type 1 which is the predominant strain in Europe, and possibly other areas of the world (including the middle east and western Asia), which is still very necessary.

there is no Pandemic. It too is a fiction. Bird Flu is indegenous to the Americas. It in no way fits the profile of a "Pandemic." It is too lethal to be a viable pathogen. It kills itself off.

That logic is simply ridiculous, with the high population densities of cities and the speed and frequency with which people travel. You're seriously suggesting that a human-transmissible bird flu wouldn't be a "viable pathogen" because it would kill everyone in Taiwan too quickly to spread? Even if that were true, which is isn't, wouldn't you expect the Taiwanese to be concerned about that?

The idea that a human-transmissible bird flu would be dangerous has already been demonstrated by the 1918 flu epidemic that killed 20-50 million people. The 1918 virus was recently reconstructed, and it was found to be very similar to the bird flu viruses that are around in Asia today. The actual scientific paper, available here states:

"Until now, the exceptional virulence of the 1918 pandemic influenza virus has been a question of historical curiosity. Herein, we demonstrate the successful reconstruction of the 1918 pandemic virus in order to understand more fully the virulence of this virus and possibly of other human influenza pandemic viruses. Because the emergence of another pandemic virus is considered likely, if not inevitable (25), characterization of the 1918 virus may enable us to recognize the potential threat posed by new influenza virus strains, and it will shed light on the prophylactic and therapeutic countermeasures that will be needed to control pandemic viruses."

Tamiflu, assuming Bird Flu were to mutate into a dangerous flu "Pandemic", would be of no value. The disease kills in about 9 days. It is symptomatic only 2 of those days. By the time a person knew they were getting sick, getting a prescription would not save them. Its value is probably null anyway as it appears it is ineffective against the disease. Its only value would be prophalaxis and that is questionable.

A scientific paper demonstrating Tamiflu's effectiveness against the H5N1 virus is here .

A paper demonstrating Tamiflu's effectiveness against the 1918 flu virus (which is similar to the virus we fear will emerge) is here.

Here's the journal abstract:

http://www.pnas.org/cgi/content/abstract/050746910 2v1

"Mars currently has no global magnetic field of internal origin but must have had one in the past, when the crust acquired intense magnetization, presumably by cooling in the presence of an Earth-like magnetic field (thermoremanent magnetization). A new map of the magnetic field of Mars, compiled by using measurements acquired at an 400-km mapping altitude by the Mars Global Surveyor spacecraft, is presented here. The increased spatial resolution and sensitivity of this map provide new insight into the origin and evolution of the Mars crust. Variations in the crustal magnetic field appear in association with major faults, some previously identified in imagery and topography (Cerberus Rupes and Valles Marineris). Two parallel great faults are identified in Terra Meridiani by offset magnetic field contours. They appear similar to transform faults that occur in oceanic crust on Earth, and support the notion that the Mars crust formed during an early era of plate tectonics."

Well, I didn't do the calculations myself:
"However, kinetic calculations predict that
small fragments of DNA (100-500 bp) will survive for no
more than 10 kyr in temperate regions and for a maximum
of 100 kyr at colder latitudes owing to hydrolytic damage
(Poinar et al. 1996; Smith et al. 2001). Even under ideal
conditions, amplifiable DNA is not thought to survive for
longer than 1 Myr." - see reference below

  As to your proposal, if I make enough random DNA out of monomers, eventually one of those artificial chains will form a complete dinosaur chromosome. How, exactly, do you propose that I identify this perfect chromosome from among the population in my (absolutely enormous) sample?

  Reference:
http://www.journals.royalsoc.ac.uk/openurl.asp?gen re=article&eissn=1471-2954&volume=272&issue=1558&s page=3

  For what you *can* do with fossil DNA, read this:
http://www.pnas.org/cgi/content/full/102/39/13783

Apparently, the answer is "yes."

Interestingly, they found evidence of rice, grapes, and honey. In this study, it is identified that the fermentation of grapes may be inferred from a by-product of grape fermentation (i.e., tartaric acid); however, the presence of honey is only inferred from compounds that point to the existence of beeswax.

in other words, although we can show that grapes were probably fermented, we have no way of saying anything other than "honey was present". For all we know, it was a rice mead with grapes!

(OK... I'm a little biased toward mead), but...

the original article (from Italy) assumes that it was "wine", not mead or hard cider that was found... and that it is the "oldest" at 5000 B.C.; no bias toward the wine industry, eh?

Proceedings of the National Academy of Sciences of the USA August 14, 2001 | vol. 98 | no. 17 | 9830-9835 http://www.pnas.org/cgi/content/full/98/17/9830 It seems to cover everything mentioned in the "Australian" article.

Actually a lot this has published since 1998.

Paper here for those who have PNAS access.

"If the alien had 2 separate glands that each spat out the components of a super-acid"

Yep, the use of two glands is how the bombardier beetle sprays 100degC acid (and other nasty stuff) out of their arse.

Offtopic - Search google for "bombardier beetle" and 3 out of the first 4 hits declare it to be "proof" that evolution is wrong. Have these people never heard of the babelfish?

Yeast has also been used to produce gold filaments.

http://www.wi.mit.edu/news/archives/2003/sl_0331.h tml
http://www.pnas.org/cgi/content/abstract/100/8/452 7

Mmm... Chips AND beer...

Here is a link to their paper:

http://www.pnas.org/cgi/reprint/0504878102v1.pdf

I can think of nothing more convincing than the evidence. Such as the nearly complete Turkana Boy skeleton, an example of Homo erectus from roughly 1.6 million years ago, as presented in this textbook on evolution. A few ribs my ass. Or how about this nice picture of a whole bunch of hominid skulls from 2.6 million years ago to the present? Teach it for real, and it doesn't take undergraduate level biochemistry. Show the kids pictures of the fossils. Tell the kids about human DNA: how our chromosome 2 is clearly the result of a fusion event between two mid-sized progenitor chromosomes, which are still seen in chimps, our closest relatives. Tell the kids that 200 years ago christian geologists went looking for evidence of the Biblical flood and instead found evidence that the Earth is ancient. While we're at it, we should show them the evidence for creationism and intelligent design, too: a deafening silence lasting 10 seconds should suffice.

You want to falsify evolution? Okay, find a bunny rabbit in the Precambrian. Sequence a mamalian genome and find out that it is more closely related to a banana than another mammal. Find a lizard that doesn't use the standard genetic code or a very close derivative of it. Find a bird with a different set of 20 amino acids. Find a chimera--for instance, a tree with 100% tree features, except that it's TCA cycle enzymes are identical to those found in mice, or if you don't want any biochemistry or genetics, find a goat with bird feathers--can't happen under evolution. Every day, more fossils are found. More genes are sequenced. More papers published, and more proteins are compared. Every day evolution is tested, as it makes specific predictions about how species are interrelated. As a result, evolution is the most thoroughly tested theory in science. Have a look at the evidence--a small portion of it is easily available for the general audience online at talkorigins . Creationism and intelligent design on the other hand are compatible with all evidence, as one can simply say "goddiditthatway" and you're good...unless you want to call it science. You want things taught in science class that are argeed on, fine. Teach evolution.

the maximum number of mutations (of any sort -- duplication, base-pair, etc) between man and the most recent ancestor of man and apes is 1,667

I was trying to find a link to justify your statement about 10% biomass, and instead I found a link that says 10-25% of biomass, depending on region. Heh, so apparently you're more than correct.

There are still some good arguments that humans will be able to weather most storms successfully, no?

• Other species aren't changing very much, but humans are changing extremely rapidly. Evolutionarily, there isn't much physical difference between Pythagoras and Einstein, except that Einstein had 2400 years more of collected human knowledge at his birth. This human knowledge continues to accumulate, and its pace is probably accelerating. This rapid change will allow humans to more quickly adapt to changes in environment than other species which either rely on pure evolution, or have a more limited intelligence.
• Human beings can plan ahead much better than other species (eg. we have a significantly better chance of spotting climate change, or see asteroids coming, etc etc).
• Space travel. We're not quite there yet, on a scale that would save us from destruction of a single planet, but we may soon be. Long term, I'd think this gives us a huge advantage in the game of evolution.

Fine, let's see the math. Let's see the trajectory calculations. How about those calculating the space? Calculating the number of dimensions the space has, and how fast that number changes over time?

I guess you'll need to read Spivey's publications for this.

In particular the paper Continuous attraction toward phonological competitors who's abstract is

Certain models of spoken-language processing, like those for many other perceptual and cognitive processes, posit continuous uptake of sensory input and dynamic competition between simultaneously active representations. Here, we provide compelling evidence for this continuity assumption by using a continuous response, hand movements, to track the temporal dynamics of lexical activations during real-time spoken-word recognition in a visual context. By recording the streaming x, y coordinates of continuous goal-directed hand movement in a spoken-language task, online accrual of acoustic-phonetic input and competition between partially active lexical representations are revealed in the shape of the movement trajectories. This hand-movement paradigm allows one to project the internal processing of spoken-word recognition onto a two-dimensional layout of continuous motor output, providing a concrete visualization of the attractor dynamics involved in language processing.

Trajectories on phase space are soooooooo sexy. But if it's any good, it'll result in something more concrete than more people picking up this flag and waving it while shouting the new slogans and buzzwords. Until that happens I peg this with the study that "calculated" the "fractal dimension" of the cortex just because it has fold and folds in the folds.... so fsking what.

Personally I think this work is quite important in identifying what is really happening in a brain processing. Its trying to test a hypothesis on a continuous model of computing as opposed to a discreet model. This is not really the same as a digitat/analogue distinction (think LP's vrs CD for that).

This has a lot to say about how we make descisions, if our brains were a discreet device then we might expect different behaviour in the experiment.

If we are to fully work with an analogue model then we do need to develop a different set of models for this. The traditional discreet boolean logic of manistreem computing today is inadaquate. Instead we need to bring on a different set of models based around dynamical systems, and related theories, of bifucation, singularities and catastrophy theories.

One question I'm particular interested in is how we convert from the continuous domain of our senses to the making a binary descision move mouse over picture A or picture B. The experiment shows that it seems to be a hardeing process with a tentative guess first which then strentherns. It can be though of as there being two stable atractors, one for each picture and they have an experiment which nicely shows trajectories through one slice of this space. There are interesting links with the Soroties paradox and hysteresis here (email me for details).

I think we'll be seeing a lot more work along this line in the years to come.

Actually, in the PNAS journal article that the Cornell News story refers to, Professor Spivey compares the data he obtained in the mouse-movement experiment to a computer simulation that uses both the TRACE model of spoken-word recognition (an old-school interactive activation model that still seems to be pumping out good data, especially for a localist model) and his own normalized recurrence attractor network (another localist statistical model). Both of these models, as well as the combined one that he creates for the simulations, are by their very nature dynamical systems models, and definitely not Turing machines.
Not totally coincidentally, Spivey is also my undergrad psych major advisor.

I'd have said "RTFA", but since slashdot doesn't directly link to the journal article PNAS, I guess you're kind of off the hook.

Wow, sounds like the end of life as we know it.

it might be used in three to five years to make devices that could detect bioterrorism chemicals.

Yeah, did I tell you about my DNA-based Cellular Autonomous Terminator ? It's very good at searching&destroying living organisms, and it already has a stealth mode, night vision and laser-based target designation. Gimme funding and I'll see what I can do about homeland security.

another team led by Weiss showed they could insert DNA into cells to make them behave like digital circuits.

OK, now that sounds interesting. But the March 8 paper is about robustness of feedback loops in biological systems. Directed evolution of a genetic circuit does have logic gates though.

But we don't need life to produce nice regular chemical patterns. See e.g. reaction-diffusion systems. The whole point of synthetic biology would be self-assembly self-replication. So wake me up with sexy headlines when we know how to compile some Turing-complete language to DNA.

Until then, editors should have a rule about anti-terror plugs in articles, e.g. "three times and you're out".

Wow, sounds like the end of life as we know it.

it might be used in three to five years to make devices that could detect bioterrorism chemicals.

Yeah, did I tell you about my DNA-based Cellular Autonomous Terminator ? It's very good at searching&destroying living organisms, and it already has a stealth mode, night vision and laser-based target designation. Gimme funding and I'll see what I can do about homeland security.

another team led by Weiss showed they could insert DNA into cells to make them behave like digital circuits.

OK, now that sounds interesting. But the March 8 paper is about robustness of feedback loops in biological systems. Directed evolution of a genetic circuit does have logic gates though.

But we don't need life to produce nice regular chemical patterns. See e.g. reaction-diffusion systems. The whole point of synthetic biology would be self-assembly self-replication. So wake me up with sexy headlines when we know how to compile some Turing-complete language to DNA.

Until then, editors should have a rule about anti-terror plugs in articles, e.g. "three times and you're out".

"Traditional" academic journals actually get very little money from commercial advertising. Many specialized field journals have been using "pay for play" models well before the Internet came along. With these journals, such as the Journal of Immunology, each article usually bears the following disclaimer:

The cost of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

I have been through the manuscript submission process and you have to pay big bucks once your paper is accepted for publication: $200 per article if you have supplemental information (material that doesn't fit in the manuscript but still published), $70 per printed page, and $325 per color figure for printing a Proceedings of the National Academy of Sciences article. If you want to allow your article on Open Access, you'll need to pony up another $750-$1000 dollars.

>Replicators aren't standalone.

Proof by forceful assertion? We've already created simple self-replicating molecules. If you have some magical theory of why such things couldn't form in nature, I'd love to hear it.

"Even looking early in the Cambrian period, fossils of the major groups of invertebrates appear in an explosion of living things, unconnected to any evolutionary ancestors."

Bilateran fossils discovered from 40-55 million years before the Cambrian.

History of the search for precambrian life

Embryonic stem cells develop into functional dopaminergic neurons after transplantation in a Parkinson rat model.

Twenty-five rats received ES cell injections, and 13 rats received sham surgery by injection of vehicle (medium). Six rats showed no graft survival and five rats died before completed behavioral assessment and were found to have teratoma-like tumors at postmortem analysis.

Of course, it still falls under under the ban on creation of new lines.

I find that most journals charge per page and charge per color figure. Typical costs can run to $2000 easily.

Ever try to cram results into a readable black and white figure? It's really hard! I think journals should offer free online color figures. Anyways, that's just about the only way I retrieve articles anymore.

Fyi, my advisor wants me to publish in PLOS Comp. Bio., but (if I have a choice) I'd rather send papers to PNAS. Another open access journal (6 months after publication). I like the idea of PLOS though and I think it'll make a good contribution to the field.

If you want a supporting argument for Genesis, it is easy enough to asser that the events in the time preceeding Adam were described to him by the almighty, recorded either orally or in writing, and finally made their way into the current text.

So you expect me to take on faith that Adam existed, spoke to god, and wrote it down and that this is the truth, but you won't except evolution because you can't see it happening. Sorry, doesn't fly. Claims are not evidence. Claiming to speak to god is not evidence that he did. And you can't hold my argument to a higher standard than you hold your own.

But the discussion is not one about creationism, rather it is one about what ideas should journalists present.

It was until you claimed creationism had valid scientific evidence to support it and failed to present any. But, you want to present both sides in a scientific discussion? Fine. Have some evidence. Mistating evolutionary theory is not evidence. Claims that it is possible is not evidence. "Ancient documents" whose very origin is dubious is not evidence. You've got no evidence, so that's what we'll present.

If you want a rational discussion, put some facts on the table.

I see little point since you can't even decide what constitutes valid scientific evidence. Anything that's possible is not probable. Just being possible is not evidence of it acutally happening. But, here's some light reading:

"Origin of Species" by Charles Darwin - the father of modern evolutionary theory. Explains in detail the concept of natural selection among others.

Strength and tempo of directional selection in the wild - a scientific study on the effects of natural selction in the wild.

Comparison of the Human and Great Ape Chromosomes as Evidence for Common Ancestry - in fact, quite a bit at this site is useful.

And I highly recommend:
Evolution and the Fossil Record - published by the American Geology Institute. Not only is it informative but highly accessible to non-scientists.

Every model of the world devised to date has eventually been discredited,

This is a flat out lie. The earth is still round and still orbits the sun, for starters. Both ideas are older than Christ. Again, misrepresenting the facts to support your argument.

I never said I was a creationist.

Yet you are so willing to take "ancient documents" on faith but discredit evolution because you can't see it happening.

And my arguments are quite rational if one looks only at the facts.

Calling the most wild-ass ideas with no evidence to support them reasonable is not rational. Requiring faith to support your argument and having none to discredit mine is not rational. Believing that anything that is possible is just as likely to be true is not rational. And even if they were, rational is not evidence. I'd love to look at the facts, but you haven't supplied any.

Perhaps we should have a neutral party review the discussion.

First, good luck finding one. Second, I don't care anymore. The main problem here, which oddly enough goes back to the original discussion, is you have no idea what constitutes valid scientific evidence. Until you can resolve that, there is no point in discussing this any further. Feel free to write the whole episode off as my unwillingness to consider what goes against the status quo. You're going to anyway, regardless of what arguments I make because it's what you want to believe, so I don't see why I should bother.

For those of you who care the research paper can be found at http://www.pnas.org/cgi/reprint/0406930101v1.pdf

I've been watching that lunatic Keilis-Borok for quite some time and you have not described his activities accurately. K-B never claimed to have accurately predicted more than the 2 quakes in Japan and San Simeon. He made a well-publicised recent prediction that there would be a 6.5 quake at a specific spot near the Mohave Desert.

Which I believe I mostly said, though I give him a little more credit than yourself. Regardless, I did say he predicted the two earthquakes in Japan and San Simeon as well as a failed prediction for the Mojave Desert (which ironically, is in Southern California).

Also, K-B was *against* announcing the prediction. The chair person of the Institute of Geophysics and Planetary Physics at UCLA urged him to announce his results. He begrudingly agreed. Throughout the prediction time frame, Dr. K-B admitted there was only a slight chance the Mojave prediction would even be right.

I read K-B's papers and analyzed his theories and they are complete horseshit, unscientific garbage. I am not a seismologist, but I used to work as a data analyst with professional seismologists, so I know what I'm talking about.

In case you'd like to really read K-B's paper of his methods, you can find it here. Using the same methods he used to predict the Japan and San Simeon quakes, he was able to backtrack and use data to show that his method could have predicted five other earthquakes. There really is nothing phony about this and it's simply good science to test your results against a "control."

I suppose I should end this with my own disclaimer: I've worked for the Southern California Earthquake Center. And like you, I also know what I'm talking about.

As a geologist, I do find the prospect of earthquake prediction quite exciting. I even worked a few doors down from Dr. Keilis-Borok (predicted Japan and San Simeon, failed prediction in Southern California) this summer at UCLA, doing some earthquake research.

Dr. K-B's approach used statistical analysis and was quite an interesting idea. His paper even correlated some previous earthquakes (such as Landers and Northridge) using his "tail-wag-the-dog" method to try and verify his results.

Anyway, regarding these latest predictions by John Rundle and his team, I decided to read the paper. You can actually find it here.

I'm not understanding how they succesfully predicted certain things or how useful his theories are. They are saying they predicted three of the earthquakes that happened in Big Bear.

From what I am understanding, the way their method works is that it shows potential "hot spots" for earthquakes for the next 10 years. That means the whole Big Bear/San Bernardino Mountains area should show up as a hotspot on their map. This doesn't mean they have succesfully predicted all 3 earthquakes though if I understand this right. They predicted the potential for one M5.0 or greater there withing the next 10 years. The fact that there were three of them is just icing on the cake I suppose?

I also can't find any information that shows how many false-positives they nailed as well. This might be kind of hard since they won't know about false-positives until after their prediction period is up in 2010. Without that data though, we can't really be sure of how good this method works. And even if it misses some, it only reduces the chance of an earthquake happening in the next X years to some percentage (which we already have certain data for from the USGS. 67% chance of a M6.7 or greater striking the Bay Area before 2030 and an 80% chance of a M7.0 or greater striking Southern California before 2030).

Admitedly, if this method is promising, it might put better constraints on the data though, so we could say something like, "97% chance of an M7.0 striking within 10 years." However, this still won't help all that much in the scheme of things.

Additional information:
http://www.sciencedaily.com/releases/2004/10/04100 5071107.htm
John Rundle's Paper

As a geologist, I do find the prospect of earthquake prediction quite exciting. I even worked a few doors down from Dr. Keilis-Borok (predicted Japan and San Simeon, failed prediction in Southern California) this summer at UCLA, doing some earthquake research.

Dr. K-B's approach used statistical analysis and was quite an interesting idea. His paper even correlated some previous earthquakes (such as Landers and Northridge) using his "tail-wag-the-dog" method to try and verify his results.

Anyway, regarding these latest predictions by John Rundle and his team, I decided to read the paper. You can actually find it here.

I'm not understanding how they succesfully predicted certain things or how useful his theories are. They are saying they predicted three of the earthquakes that happened in Big Bear.

From what I am understanding, the way their method works is that it shows potential "hot spots" for earthquakes for the next 10 years. That means the whole Big Bear/San Bernardino Mountains area should show up as a hotspot on their map. This doesn't mean they have succesfully predicted all 3 earthquakes though if I understand this right. They predicted the potential for one M5.0 or greater there withing the next 10 years. The fact that there were three of them is just icing on the cake I suppose?

I also can't find any information that shows how many false-positives they nailed as well. This might be kind of hard since they won't know about false-positives until after their prediction period is up in 2010. Without that data though, we can't really be sure of how good this method works. And even if it misses some, it only reduces the chance of an earthquake happening in the next X years to some percentage (which we already have certain data for from the USGS. 67% chance of a M6.7 or greater striking the Bay Area before 2030 and an 80% chance of a M7.0 or greater striking Southern California before 2030).

Admitedly, if this method is promising, it might put better constraints on the data though, so we could say something like, "97% chance of an M7.0 striking within 10 years." However, this still won't help all that much in the scheme of things.

Additional information:
http://www.sciencedaily.com/releases/2004/10/04100 5071107.htm
John Rundle's Paper

I'll refer you to an excellent article(FULL free text on pubmed as a bonus) at http://www.pnas.org/cgi/content/full/98/18/10214. Table 2 is of great interest; it displays probabilities of sexual-mediated infection for every kind of partner, male to female or female to male (sadly, male/male is absent from the list). Notice the sad looking rate of infection (0.04) in normal partners (HIV-1 is a lousy virus, efficiency speaking... thank god!). The rates are a lot smaller in delta32 individuals (table show data for homo or heterozygotes), especially in transmission from a non-acutely (first stages of the disease, where the virus replicate a lot, then fade for 10-20 years before destroying the immune system) infected partner.

Other means of infection include of course intraveinous drug, which can transmit a T-tropic virus which is fully infectious in these individuals (infect T cells but not macrophages) and blood transfusions (in the 80s, mainly).

In recent years, lots of efforts have been made to give robots the ability to hear and see. But what about the sense of touch? Unlike us, robots don't have sensitive skin. But this is about to change. By using organic, or plastic, field-effect transistors as pressure sensors deposited on a flexible material, researchers at the University of Tokyo have created an artificial skin which will give robots the sense of touch . The prototype has a density of 16 sensors per square centimeter, far from the 1,500 of our fingertips. When this density increases and when the problem of the reliability of this kind of transistors is solved, the researchers say this artificial skin will also be used for car seats or gym carpets. Expect to see them in four or five years. Read more...

Here are selected excerpts from the Technology Research News article.

Researchers from the University of Tokyo have devised pressure-sensor arrays that promise to give objects like rugs and robots the equivalent of one aspect of skin -- pressure sensitivity.

The researchers' pressure sensor arrays are built from inexpensive organic, or plastic, transistors on a flexible material. This allows for dense arrays that can be used over large areas.

The arrays could be used in pressure-sensitive coverings in hospitals, homes, gyms and cars to monitor people's health and performance, and eventually as skin that would give robots the means to interact more sensitively with their surroundings, said Takao Someya, an associate professor of electrical engineering at the University of Tokyo.

The sensor skin works even when rolled around a cylinder as small as 4 millimeters in diameter, said Someya. The researchers' prototype is an eight-centimeter-square sheet containing a 32-by-32 array of organic sensors -- a density of 16 sensors per square centimeter. In contrast, humans have 1,500 pressure sensors per square centimeter in the fingertips, though far fewer in most other places.

And what are possible applications?

The active-matrix design allows the arrays to be smart enough to enable specific sensors at certain feedback points to, for instance, monitor the heart and breathing rate of a hospital patient who has fallen to the floor, said Someya. The skin could measure whether an elderly patient is just taking a rest, or needs help, he said.

The skin could also be used in car seats to monitor drivers' mental and physical conditions, Someya said. "Our large-area pressure [sensing abilities] would be helpful" in obtaining information through drivers seats, he said.

And, of course, we'll see home robots able to pick an egg in the fridge.

The research work has been published by the Proceedings of the National Academy of Sciences on July 6, 2004, under the title "A large-area, flexible pressure sensor matrix with organic field-effect transistors for artificial skin applications." Here is a link to the abstract .

First off, let me say that there is really no ambiguity about the structure of DNA anymore. Structures of DNA have been determined by x-ray crystallography, NMR, and to lower resolution, electron microscopic methods. The kinetics of the binding of DNA strands to one another has been studied in detail (and naturally the kinetics would be very sensitive to differences in the number of strands found in the structure).

Most of the x-ray structures which have been solved have used multiple heavy atom derivatives, which relieves the ambiguity of the Bessel function solutions that you referred to IIRC. Also, many of the structures which have been solved show DNA bound to the proteins which bind it in vivo. Since the structure is antiparallel double helical when bound to these proteins (and in general, the structures are consistent with large numbers of biochemical and genetic experiments on the proteins and DNA sequences in question), one has to assume that the Watson-Crick structure is generally correct.

I don't follow your thread-tying experiment, despite a degree in biochemistry. Eukaryotic DNA (which includes the DNA that Franklin, Wilkins, Watson & Crick worked on, I believe) is linear. Thus, you shouldn't be tying *any* of the threads together.

Bacterial DNA and some viral DNAs are circular, but the correct way to model them is to twist a black and white thread together, then tie them, black to black and white to white.

Anyway, you are raising the issue of topological transitions in DNA. This is a well understood and extensively studied issue. In fact, there is even a good mathematical formalism for it. For the math, see (sorry, no full text for these):

FB Fuller, The Writhing Number of a Space Curve, PNAS 68(4) 815-819, 1971
http://www.pnas.org/cgi/content/abstract/68/4/815

FHC Crick, Linking Numbers and Nucleosomes, PNAS 73(8) 2639-2643, 1976
http://www.pnas.org/cgi/content/abstract/73/8/2639

FB Fuller, Decomposition of the Linking Number of a Closed Ribbon: A Problem from Molecular Biology, PNAS 75(8) 3557-3561, 1978
http://www.pnas.org/cgi/content/abstract/75/8/3557

So, the need for de-linking enzymes has been appreciated for some time, and enzymes that catalyze that reaction have been identified and characterized. In fact, inhibitors of these enzymes (called topoisomerases) are used in treating cancer and bacterial infections. For more recent references and explanations, see:

http://www.maich.gr/natural/staff/sotirios/topo.ht ml
http://cmgm.stanford.edu/biochem201/Handouts/DNAto po.html
http://crab.nyu.edu/~alex/mypapers/MolBiolRev.pdf

First off, let me say that there is really no ambiguity about the structure of DNA anymore. Structures of DNA have been determined by x-ray crystallography, NMR, and to lower resolution, electron microscopic methods. The kinetics of the binding of DNA strands to one another has been studied in detail (and naturally the kinetics would be very sensitive to differences in the number of strands found in the structure).

Most of the x-ray structures which have been solved have used multiple heavy atom derivatives, which relieves the ambiguity of the Bessel function solutions that you referred to IIRC. Also, many of the structures which have been solved show DNA bound to the proteins which bind it in vivo. Since the structure is antiparallel double helical when bound to these proteins (and in general, the structures are consistent with large numbers of biochemical and genetic experiments on the proteins and DNA sequences in question), one has to assume that the Watson-Crick structure is generally correct.

I don't follow your thread-tying experiment, despite a degree in biochemistry. Eukaryotic DNA (which includes the DNA that Franklin, Wilkins, Watson & Crick worked on, I believe) is linear. Thus, you shouldn't be tying *any* of the threads together.

Bacterial DNA and some viral DNAs are circular, but the correct way to model them is to twist a black and white thread together, then tie them, black to black and white to white.

Anyway, you are raising the issue of topological transitions in DNA. This is a well understood and extensively studied issue. In fact, there is even a good mathematical formalism for it. For the math, see (sorry, no full text for these):

FB Fuller, The Writhing Number of a Space Curve, PNAS 68(4) 815-819, 1971
http://www.pnas.org/cgi/content/abstract/68/4/815

FHC Crick, Linking Numbers and Nucleosomes, PNAS 73(8) 2639-2643, 1976
http://www.pnas.org/cgi/content/abstract/73/8/2639

FB Fuller, Decomposition of the Linking Number of a Closed Ribbon: A Problem from Molecular Biology, PNAS 75(8) 3557-3561, 1978
http://www.pnas.org/cgi/content/abstract/75/8/3557

So, the need for de-linking enzymes has been appreciated for some time, and enzymes that catalyze that reaction have been identified and characterized. In fact, inhibitors of these enzymes (called topoisomerases) are used in treating cancer and bacterial infections. For more recent references and explanations, see:

http://www.maich.gr/natural/staff/sotirios/topo.ht ml
http://cmgm.stanford.edu/biochem201/Handouts/DNAto po.html
http://crab.nyu.edu/~alex/mypapers/MolBiolRev.pdf

First off, let me say that there is really no ambiguity about the structure of DNA anymore. Structures of DNA have been determined by x-ray crystallography, NMR, and to lower resolution, electron microscopic methods. The kinetics of the binding of DNA strands to one another has been studied in detail (and naturally the kinetics would be very sensitive to differences in the number of strands found in the structure).

Most of the x-ray structures which have been solved have used multiple heavy atom derivatives, which relieves the ambiguity of the Bessel function solutions that you referred to IIRC. Also, many of the structures which have been solved show DNA bound to the proteins which bind it in vivo. Since the structure is antiparallel double helical when bound to these proteins (and in general, the structures are consistent with large numbers of biochemical and genetic experiments on the proteins and DNA sequences in question), one has to assume that the Watson-Crick structure is generally correct.

I don't follow your thread-tying experiment, despite a degree in biochemistry. Eukaryotic DNA (which includes the DNA that Franklin, Wilkins, Watson & Crick worked on, I believe) is linear. Thus, you shouldn't be tying *any* of the threads together.

Bacterial DNA and some viral DNAs are circular, but the correct way to model them is to twist a black and white thread together, then tie them, black to black and white to white.

Anyway, you are raising the issue of topological transitions in DNA. This is a well understood and extensively studied issue. In fact, there is even a good mathematical formalism for it. For the math, see (sorry, no full text for these):

FB Fuller, The Writhing Number of a Space Curve, PNAS 68(4) 815-819, 1971
http://www.pnas.org/cgi/content/abstract/68/4/815

FHC Crick, Linking Numbers and Nucleosomes, PNAS 73(8) 2639-2643, 1976
http://www.pnas.org/cgi/content/abstract/73/8/2639

FB Fuller, Decomposition of the Linking Number of a Closed Ribbon: A Problem from Molecular Biology, PNAS 75(8) 3557-3561, 1978
http://www.pnas.org/cgi/content/abstract/75/8/3557

So, the need for de-linking enzymes has been appreciated for some time, and enzymes that catalyze that reaction have been identified and characterized. In fact, inhibitors of these enzymes (called topoisomerases) are used in treating cancer and bacterial infections. For more recent references and explanations, see:

http://www.maich.gr/natural/staff/sotirios/topo.ht ml
http://cmgm.stanford.edu/biochem201/Handouts/DNAto po.html
http://crab.nyu.edu/~alex/mypapers/MolBiolRev.pdf