Neandertal genome? Or a premature announcement?

We will be able to tell whether it is a premature announcement when time comes for the paper, of course.

I really, really hope they clone one. Screw the ethics - it would just be cool.

I saw this at a science web site last night. There is a second group working on a different individual, but far less complete. I thought it was a bit premature to announce to MSM. But still, there should be some interesting findings when they are all done.

Nerd of Redhead, OM/#3: I think I saw that too - the headline (at least in iGoogle) is incredibly misleading. I got all excited and thought the entire genome was complete. But no. Still, I can't wait to see their findings when it's finished.

Between the problems with degradation, and especially that of contamination with modern human DNA, one does need to be cautious regarding such an announcement.

I know that it used to be that they were only sure about a sequence when it differed from our own, since they were always sequencing human DNA along with neandertal DNA, and I can't help but think that no one has reduced contamination to very acceptable levels, especially where a short sequence is exactly the same as our own.

Glen D
http://tinyurl.com/6mb592

I don't mean this as a challenge at all, I'm genuinely asking, what's the point?

Don't forget to read Genomicron! I posted a link to the press conference with Svante Paabo...

View here

They can check it against mine. My wife is always calling me a Neandertal and she's always right.

@2 My thoughts too. Except what if we find (after cloning) that Neanderthal is just another word for religious zealot?

I just sent off my DNA genealogy test a couple of days ago (it was on sale, and I'm a little curious.)

I wonder if the Neanderthal genome will end up in the same database, so I can see how closely related I am? ;)

The point, to answer Marc's (#6) question, is that an analysis of the genome might answer some questions such as "did the Neandertals have language?" or perhaps "did modern humans and Neandertals interbreed?"

"I don't mean this as a challenge at all, I'm genuinely asking, what's the point?"

You have GOT to be kidding.

I'm curious to find out if they had 23 or 24 chromosomes.

No, I was not kidding. I had the same questions about bear genomes too during the election but the howls of outrage and derision directed at McCain dissuaded me from asking.

Thanks Aaron #11, I did anticipate that it would provide answers for natural historians and anthropoligists, I was just hoping that it might give some other answers too and perhaps have some practical benefits thrown in for good measure.

Clone one. This is a must. Then ask the Christians whether it has a soul. Just one of the obvious ways that evolution and Christianity are completely incompatible. For all the theistic evolutionists out there, explain neandertals. And if they do have souls, why did god let them die out long before the salvation of Christianity?

By the way, the site is telling me my spelling of neandertal is wrong. Is this correct, or are there multiple spellings?

(It also gives me the option of changing to 'Netherlander', which I think is a bit harsh.)

bunnycatch3r @ 9

Ha, that would be a new species, irrespective of evolution!

"I was just hoping that it might give some other answers too and perhaps have some practical benefits thrown in for good measure."

Well, worded this way I see your question differently... I guess you were asking "what are the benefits," etc.

I'm more used to the phrase "what's the point?" being used as a way of saying "why bother? who cares?"

I really, really hope they clone one. Screw the ethics - it would just be cool.

Let's see... he/she would be a lab rat equivalent or a zoo exhibit? Soul or no, wouldn't this be inneanderthale?

"...and it's all entirely from one specimen."

Not quite true. According to one of the articles, "The genome is compiled from three shards of limb bone from Vindija Cave that turned out to be from two females."

@Marc Ambian

Some people think genetic history is interesting. If you find neither genetics nor history interesting, I guess you have a case to make.

What I want to know is, if we were to clone some neanderthals, and let them grown naturally, would they be excellent at croquet, as Jasper Fforde predicts?

Let's hope the press doesn't interview the likes of Ray Comfort (which the BBC did yesterday for Darwin Day). They let Ray babble about dog sexes or something like that. I have to say he's more irritatingly vacuous when speaking than he is when writing his craptastic blog entries.

I'm on board about suspect science-by-press-conference style announcements. But Svante Paabo is a pretty stand-up scientist in my experience.

I don't mean this as a challenge at all, I'm genuinely asking, what's the point?

If you're asking what practical point there is, likely there is not too much. With bear genetics it is important to understand how much outbreeding exists among populations, that is to say, if they are genetically healthy. Inbreeding is death.

Yet even with neandertal DNA sequencing there may be some practical uses, for they may have evolved somewhat different ways of coping with cardiovascular problems, or the like. This could lead to treatments of modern humans, though probably not through genetic engineering of humans. Whether they had adaptations to fight malaria or other infectious diseases could give us some record of those diseases, and tell us how much we adapted to fight infectious disease.

Scientifically and humanly, it's extremely interesting. I've never thought it likely that neandertals did not speak (how do you have that much technology and culture without speaking?), but we might find out how well they spoke from studies of morphology and genetics. That could have some bearing on how well our own ancestors spoke.

And just how did neandertals adapt to a cold environment? We're not well adapted to it, but they had much longer to evolve to cope with the cold (and didn't have our technology). Did they have special adaptations for eating diets heavy in meat?

Basically, we'd like to know how much flexibility exists in primate phenotypes/genotypes. Can small tweaks, like the differences between neandertals and humans, make large changes in phenotype, or were they truly a lot like us?

Plus, they had bigger brains, on average, than we do. Why? Were they quite intelligent as we count intelligence, or were they perhaps not intelligent in our way, but in quite another way? If we can tease out the answers, we might know more about what makes a human intelligent, or deficient in intelligence (other than adhering to creationism).

Most of what we're interested in is not likely to yield much practical benefit, although it seems likely that we'll benefit medically from studying neandertals, somewhat. However, the whole "what makes us human," and what made neandertals different, is the major question that we want to answer from such study.

Glen D
http://tinyurl.com/6mb592

Well, worded this way I see your question differently... I guess you were asking "what are the benefits," etc.

Of course I hoped there would be practical benefits (I consider any knowledge a benefit), but I did just want to know what kind of questions could be answered with this genome. A greater understanding of evolutionary history I had guessed, but I wondered if it would answer some questions about human genetics instead of just ones like did neandertals interbreed.

I'm more used to the phrase "what's the point?" being used as a way of saying "why bother? who cares?"

I know. I was just trying to make sure I was answered.

Svante Pääbo is a pretty bang up researcher, agreed, but I'm annoyed that he or his bureaucratic handlers (Be it department, or whathave you) decided to engage in this science by press release. This is not how it works. There's lots of reason to be /very/ cautious when it comes to ancient DNA work, and this strikes me as more than slightly jumping the gun.

Ah, well, C'est la vie.

You'd certainly never (legally (or ethically)) be able to start with humans and clone a neanderthal? But, what if you started with some other primate and worked towards a neanderthal, a la the elephant-to-mammoth approach discussed a little while ago? Would that be "okay" (to use a small, loaded word)? I have no idea, myself.

What's the point???!!

What's the point of learning anything that doesn't put food down your pie hole or change the channel on your bigscreen without having to get your fat ass off the couch?

What's the "point" of making art? What's the point of writing music or poetry? What's the point of Jazz, or dance or good food or fine wine?

What's the bloody point of life itself?

The point of learning is learning. It's man's quest to understand himself and the universe he finds himself in. To live in a larger, more understood and more illuminated world.. and to bring light to the world. That's what the point is. The point is to NOT be a caveman and climb out of the darkness and into the light of knowledge.

Also Neandertals were immune to cancer, so there's a cure in the genome waiting to discover if we sequence that.

Just kidding. But that's the "point" of any pure research. The point is, we don't know what we'll find. It's exploration. It's Columbus. It's Magellan. It's Neil Armstrong.

You'll never learn anything new if you don't look in uncharted territory. If we already knew what the "point" was, then we'd never need to explore anything ever. We'd already know the answer before we looked.

And I'll echo the other people in saying if you don't think history, biology, genetics, anthropology etc aren't interesting or don't shed light on the ongoing human condition and enlightenment of man about life on earth... then what the fuck are you doing reading Science Blogs?

Oh, matt Neandertal is a more correct spelling (and pronunciation) of neanderthal. Well, I guess either side has a case they might make about which is right. Culturally everyone says Neanderthal. But my physical anthropology teacher in college said neandertal, and most scientists I've met say that. So I say that. What a poseur I am.

Also re the "why study bear dna" question. I think they were studying it to figure out what kind of genetic diversity they had in various populations of north american bears so that they could battle against extinction.

Now if you don't like bears, or you want them extinct, or you think they should go extinct without us learning as much about them as we can before that time... then perhaps you should (and did) vote for McCain.

Glen just spelled it all out, but I thought I might add one additional perspective.

Currently we have limited technology to understand the implications of genetic codes without observing them in practice. We might eventually be able to get a few Neandertal cells working without running into many ethical implications, and that would allow us see if they had (have?) novel adaptations to common problems. Alternately, we might be able to develop good enough models that answer the same questions.

In either case, Neandertals were very similar and had to solve many of the same problems we do, so they might have had an alternate and superior solution to resistance to common diseases that we could learn from.

Oh ffs, even if no new cure/treatment of human disease ever comes out of this: humans do science because we're curious. about everything. that's what basic research is, that's what manned space exploration is: humans wanting to know more than they already do, even if it's not very practical at all.

At the risk of hijacking this thread, I would like to get some comments on the science by press release phenomenon.

I have recently noticed that there seems to be a different kind of pressure on grant writers to succeed. It is no longer "publish or perish", but "publish and get some good press or perish".

I wonder if this change is endemic to shifting goals of major agencies. Analogous to the stock markets' preferential concern for tomorrow's earnings over next year's earnings, have the grant agencies (NIH, NSF, etc) become caught up in short term hype and marketing?

I suspect (just a hunch) that there is a shift towards a market driven approach to science, intent on squeezing every last drop of research out of our institutions. The problems characteristic to such approaches, specifically press releases and hype, are the results we are seeing.

Incidentally, when the "h" did they change the spelling of neanderthal/tal?

Of course we should clone her. And I'd be the perfect guy to attempt any interbreeding. I've got brow ridges, I'm inarticulate, my arms are twice as long as my legs ... picture a gorilla who just shaved. Build her and I will come.
Imagine the football stars! Imagine the religious nuts! Imagine the people we could falsely blame all crimes on. Imagine the unpaid plantation labor!
And they could all be easily talked into that Amway scam. This is so great!

Siamang: Neandertal or Neanderthal?

AFAIK it was always spelled with the 'h': Neanderthal.

However, from Wikipedia:
Neanderthal is now spelled two ways: the old spelling of the German word Thal, meaning "valley or dale", was changed to Tal in 1901, but the former spelling is often retained in English and always in scientific names, while the modern spelling is used in German while referring to the valley itself. (my emphasis)

Since it is a German word, it is pronounced 'tal', not 'thal' - so the confusion is perfectly understandable.

re my last post: Americans will, of course, spell it as phonetically as possible, and insist that they have the correct spelling. Hence PZ's use of 'tal' in the header.

Incidentally, when the "h" did they change the spelling of neanderthal/tal?

"Thal" is an old-fashioned German spelling of the modern word "Tal", meaning "valley". Both spellings are pronounced "Tal", as neither the voiced nor unvoiced English "th" sounds are in modern German. So "tal" is simply a more modern spelling that does not risk misleading English speakers as to pronunciation.

As for what's the point of studying other genomes, other commenters have done a fine job of defending knowledge for its own sake, so I'll take a different, purely applied, tack.

For the sake of analogy, you can think of genotypes and phenotypes as multi-variate equations, where a whole group of variable genes on one side add up to a phenotype on the other side of the equation. I know this analogy is imperfect, as genotypes and phenotypes do not vary in a one-to-one and onto way, but it's just an analogy.

Say that we want to "solve" this set of "equations" to figure out how to treat or prevent certain disease phenotypes. Let's also say this is a series of equations with 25,000 variables (genes).

How many distinct equations do we need to "solve" a set of equations with 25,000 variables? With the human genome, we have only one "equation", so we're kind of stuck. More and different genomes give us more and different "equations", and access to solving more variables, to figure out the role of these genes in health and disease phenotypes, which is a very practical and applied reason to get more data from more genomes.

@Jafafa Hots #32

The name Neandertal comes from the fact that they were found in the Neander Valley, near Düsseldorf, and the German word for valley is Tal (cognate with English "dale"), formerly spelled Thal. I think the th indicated an aspirated t. Pretty sure German never had a dental fricative (like English th), or at least hasn't had it in a long, long time. The German spelling reform of 1901 changed th -> t across the language. Scientific names aren't affected by local spelling reforms, so the scientific name is still Homo neanderthalensis.

Don't worry, they have it.

Ok, so I can buy that we are descended from an Ordovician Nautiloid - but NO WAY are we related to a this, this... monkey!

Pieceing together a genome is so easy anymore even a caveman could do it.

Yet one more line of reasoning for studying Neanderthals: They are extinct, and, despite our best efforts we are extant. What was lacking in their genetic tool kit? Curious minds wish to know.

"Yet one more line of reasoning for studying Neanderthals: They are extinct, and, despite our best efforts we are extant. What was lacking in their genetic tool kit? Curious minds wish to know."

I'm betting Homo Sapiens missionaries were sent in to convert them, and they couldn't take it.

to Marc@14

There are probably dozens of practical applications out there waiting, but it's quite impossible to tell you right now exactly what they would be. It is possible that understanding their immune system would lead us to breakthroughs in understanding our own. We could learn more about ourselves and other extant species by examining, in fact I find it difficult to think of a field that might not be impacted by the completion of the genetic sequencing.

It's also possible that we don't learn anything new that might help us practically speaking, but I think it's pretty freaking cool anyway: learning something new is its own reward.

Now that we got used to hear "draft genome" ad a proxy for "complete genome" we get "rough draft". For my next "small genomic survey" I'll announce as "really rough draft complete genome"

I don't mean this as a challenge at all, I'm genuinely asking, what's the point?

Well, I for one can think of loads of uses for an army of cloned caveman slaves.

(And I wouldn't be surprised if Jonathan Coulton isn't writing a song right now about this very possibility...)

And I'll echo the other people in saying if you don't think history, biology, genetics, anthropology etc aren't interesting or don't shed light on the ongoing human condition and enlightenment of man about life on earth... then what the fuck are you doing reading Science Blogs?

Provided the double negative was accidental, you've stumbled onto the truth there.
I merely asked what the point was so I could get the responses like #23 and #43 (thanks by the way) and understand what this means.

That first paragraph of my last post was a quote from #27. I thought that I had put in blockquote tags...

I read somewhere that this is a 60% or so 1x coverage of the genome - a good start.

What I am more interested in is the amount of the genome with 2x or more coverage. i.e. where we have some confidence in the precise base sequence, know it isn't modern contamination and can completely discount base changes due to age.

Any idea how much is up to this standard?

I do love the idea that Neanderthal man ("a modern human with rickets" apparently) has 0.5% difference, while a chimpanzee is a separate species with a mere 1.3% difference in DNA. For me this blows the micro/macro-evolution dichotomy out of the water.

Marc Albion-

Also on the bear DNA thing (I don't think anyone brought up these two points, but I just skimmed the comments) I remember a lot of the annoyance was that, in addition to the fact that his comments indicated a fundamental lack of understanding of the use of DNA in population studies, which is worrisome, 1) the study indicated that there were more grizzlies than previously estimated (Like a two fifty estimate and a five hundred actual? This is off of the top of my head), that this could actually move the bears away from their current protected status (something you'd think Palin and McCain would, you know, like, since it would open up bear areas for development and remove, or was it decrease? the fines for shooting them), and 2) he voted for that bill. Also it was part of a pattern of denigrating all science spending - who can forget the fruit fly nonsense? Anyway, that's my recollection as to why everyone got all twitchy whenever it came up.

Marc Abian, bear hater.

Apologies for the double-negative, and the over dramatic language. It's cool. I wasn't addressing you as much as addressing any particular reader who has a "why care" attitude to pure (as opposed to applied) research.

And I've met them. And my "but we might find a cure for cancer, but you'll never know if you never look..." line is a good one for them.

Plus Fuck bears. Really. They keep stealing my hunny.

...then what the fuck are you doing reading Science Blogs?

Siamang, maybe he's actually trying to learn something. The welcoming tone of your response certainly gives him an incentive to keep reading, and to keep asking those questions.

Please keep up the good work.

I'm guessing that's sarcasm from someone who didn't seem to detect mine.

I was using histrionic language for comic effect. I'm pretty aware that he is a longtime reader to Science Blogs, and this one in particular. In which case, he doesn't scare off that easily.

I'd like to see what kind of unique transposons Neandertals had - hell, maybe we could mobilize some Neandertal transposons into human cells. Sort of a rough draft of cloning!

Also, what is the layout of their liver alcohol dehydrogenase genes (like, how many, and how regulated?). Did they brew?

Anyone read "Dance of the Tiger" by Bjorn Kurten? He was Professor of Paleontology at the University of Helsinki, but this is a novel, about interaction between Neandertals and anatomically modern humans in Scandinavia 35,000 years ago. There's a sequel, "Singletusk", which I haven't read. "Dance" is a good story in its own right, but one of the themes is that we and they could (and did) interbreed, but produced sterile hybrids - who for reasons explained in the novel, are rejected by the "blacks" (our ancestors), but revered by the "whites" (Neandertals) - hence the latter's extinction.

Stephen Oppenheimer's The Real Eve: Man's Journey Out of Africa has interesting stuff about anti-Neandertal prejudice: we really don't know whether they were less intelligent than us, equally so, or more so. My hunch is that they were as individuals at least equally intelligent - as their large brains suggest - but that their greater nutritional requirements put them at a disadvantage once technology reached a certain level: smaller population per unit area, so smaller social groups, so a group could collectively remember less. (Note that even the "moderns" of those days were on average slightly more robust than people today, and slightly more sexually dimorphic, though genetic and environmental causes for this are hard to disentangle.)

but there's no report of any detectable regulatory differences.

Does this mean that they are not comparing the non-coding DNA or that is the same?

And how many humans have had their DNA entirely sequenced?

Also are we talking about Mitochondrial DNA nuclear DNA?

Randy, read the news articles. You will know as much as we do.

Please educate a poor non-biologist. I know the womb environment influences development strongly. Any cloned Neanderthals would grow in human wombs, use human cells as DNA receptors, etc. How different would they be from real Neanderthals? Would we be able to predict the differences, or identify them after the cloning?

In a related question, given a new genetic code of a Homo species (different from s. and n.) but no morphological evidence, how much would we be able to predict about that species' phenotype?

By the way, where do I sign up to be a surrogate mother to one of these? I am so there! Seriously. I can't imagine anything cooler than totally blowing someone's mind when they start fawning over me and asking if it's a girl or a boy and I say, "It's a caveman, wanna touch it?!".

Daniel Armak @59: Actually those are decent questions. First the idea of cloning a neanderthal is pure sci-fi at this point. The issue you are getting at is epigenetics. In addition to the DNA there are a number of regulatory proteins bound to the DNA. How these switches are set has a major effect on development.
Also the chemistry of the host cell notably the proteome, would play a role. Assuming we solve the significant technical challenges of turning the genome into the full complement of chromosomes with switches set to just fertilized H. sap. egg standard, (largely unknown) the results would depend on how similar H. sap and H. nean. were,...er are.
Shorter answer: Who knows?

Cold fusion was a debacle. It was replicated in hundreds of labs, and these replications were published in mainstream, peer-reviewed journals such as J. Electroanal. Chem. I suggest you review this literature before commenting on the research. You will find a list 3,000 papers on this subject here:

http://www.lenr-canr.org/

Sorry, I meant to say cold fusion was NOT a debacle.

The only problem with cold fusion has been that people pontificate about it without reading the scientific literature, and without knowing anything about it. I do not understand why so many scientists make assertions about this subject without first reading peer-reviewed journals.

Jed, science eventually straightened out cold fusion, as many of us knew it would. So what is your point?

Yes, science did straighten out cold fusion, although unfortunately some influential people such as the editor of the Scientific American still claim it was not replicated.

But there was no "debacle" at the beginning. A paper was in print, a press conference was held, which you can see on YouTube. It was reasonable, responsible, low key -- not overstated or hyped. Naturally it generated a lot of excitement.

Unfortunately cold fusion generated a firestorm of academic politics and opposition, which ruined the careers and lives of many good scientists. That was a debacle. It continues to this day. People have blamed the press conference for this outcome, but I think a low-key, informative press conference was appropriate for a breakthrough of this magnitude.

Jed, you are reporting what happened (I'm a chemist and remember our dark days very well). So what was your point? I appear to be missing it. If I am, so are others.

Guess who was working at the University of Utah when Pons and Fleischmann made their announcement? Yours truly. I followed the scientific developments very closely, since it was so near to home (the building next to ours!) and it was the major topic of conversation for quite some time.

It failed to be replicated in the sense of demonstrating any robust evidence for fusion. It was the polywater of our time.

Hmm.. premature publication. isn't there a treatment for that? I mean, it happens to all men sometimes, doesn't it ?

Err uh... wait. I think I'm confused.

@Marc#14

Think of it this way, it is human to ask what are we? what make us human, what is it to be human? Our genome sequence was interesting and we are mining interesting stuff from it comparing it with the chimp genome but one comparison is under powered for this stuff. It used to be that there were many humans on this planet, the Homo bush was twiggy. AT one time there was us, Neanderthals, Homo erectus, Homo floresiensis and maybe some 'Anatomically modern' H. sapiens. Now there is only us and when it comes to understanding us that is a bit of a problem.

Look at it like this, comparing our genome to a chimps allows us to peer at the common ancestor of both humans and chimps. Comparing our genome with that of a Neanderthal allows us to peer at Homo heidelbergensis. A much finer level of interest.

Svante's neanderthal group has been publishing for many years now and working unbelievably hard to get this done. They came out with a complete mitochondrial genome with high coverage last year, have reported on multiple genes like FOXP2, and were hit hard on contamination issues a few years ago and have now spent a lot of time working out the problems, which Svante explained at the conference. The upgrades on 454 and Solexa have made it possible to massively speed up the sequencing process so I think that many papers won't be far off. They should have higher coverage soon.

I agree that it seems weird to have a press conference before releasing a paper, but I think it generates interest in the subject and "warms people up" for the big papers. It also, I guess, had something to do with Darwin Day.

PZ Myers wrote:

"It failed to be replicated in the sense of demonstrating any robust evidence for fusion. It was the polywater of our time."

That is completely incorrect. You need to read the peer-reviewed literature before commenting on this research. Hundreds of papers were published in physics, plasma physics and electrochemistry journals describing replications at high s/n ratios, at lab such as Los Alamos, China Lake, BARC, Mitsubishi and Toyota. Over 200 groups confirmed the excess heat, and roughly 100 confirmed tritium, neutrons, transmutations and other effects (with some overlap in groups). Tritium has been measured in some cases in massive amounts, millions of times over background. Heat has been measured with no input power and over 100 W of output power lasting for days. Such results cannot be experimental error.

I find it odd -- and discouraging -- that I must plead with professional scientists to first read peer-reviewed literature before commenting on research. Any research, in any field. That is one of the ground rules of science. It does not surprise me when reporters mistakenly dismiss cold fusion as "polywater" but scientists are supposed to know better. It is easy to review the literature. You will find thousands of papers on cold fusion in a university library, and I have uploaded ~500 of them.

It would also be a good idea to read Felix Franks' book "Polywater" (MIT press). Polywater was more complicated and interesting than people realize. It was a mistake made by one group at one lab, and partially "replicated" (mistakenly) by one other lab, at what they thought was a very low s/n ratio. It was nothing like cold fusion, which has been replicated at high s/n ratios by ~2,000 researchers.

Ah, now I get it. Jed is a cold fusionist. Jed, where is your cold fusion power plant?

The only possible excuse for the news release this far ahead of a complete genome (aside from error) is advertising for research funds. Either Paabo feels he needs to stay in the limelight to justify his work (unlikely) or 454/Roche feel they need more attention for their deep sequencing platform, as against Solexa (Illumina) or Solid (ABI). This is all about money and virtually none about science. If you can't
look at the primary data, it is clearly not about science. We need to stop this kind of blatant public relations journalism and start getting serious about data availability, IMHO.

Bert Gold

So what was your [Jed's] point?

I think Jed's point is that cold fusion is being blocked by the usual suspects. Illuminati, Bilderburgers, Knights Templar, Bigfoot, and of course, the Grey Aliens.

Also that his tinfoil hat is at the laundry and things are a bit confused right now.

Cold fusion is obsolete anyway. It has been superceded by zero point energy and perpetual motion machines.

Actually, cold fusion was blocked by inability of the same experiment to show both excess heat and the right amount of neutrons that would show fusion had occurred to account for the heat. As far as research goes, if he isn't a crank, Jed could set up his own little cell and go to town, running all the experiments he wants. If he is a crank, he would expect other people to do the work.

Nerd wrote:

"Actually, cold fusion was blocked by inability of the same experiment to show both excess heat and the right amount of neutrons that would show fusion had occurred to account for the heat."

That is not a limitation, it is an observation. It was obvious from day 1. Since experimental observations overrule theory, this is a surprise, not a problem. It does not disprove or even call into question the other nuclear evidence such as heat without chemical changes, tritium, and helium commensurate with the heat.

"As far as research goes, if he isn't a crank, Jed could set up his own little cell and go to town, running all the experiments he wants. If he is a crank, he would expect other people to do the work."

If you review the experimental literature, you will see that this is very difficult, expensive and time consuming experiment, that can only be performed in well-equipped labs by experts. Prof. Richard Oriani told me that in his 50-year career, this was the most difficult experiment he ever did. The notion that I could set up "my own little cell" and do this is like suggesting that you can make a Pentium processor in your kitchen, or clone a sheep. In any case, those little cells, calorimeters, mass spectrometers and other equipment used in these experiments cost anywhere from $100,000 to $10 million, so I could not afford one. You can see photos of the cold fusion experimental appartus at the Italian Nation Nuclear Labs and the Japanese Nat. Synchrotron Lab. at LENR-CANR.org. You will see that it is not cheap, and not something you can build at home.

Comments like this reveal that you have no idea how difficult the experiment is, or how it is done. You people really need to stop pontificating about this and READ THE SCIENTIFIC LITERATURE before commenting. Why is that such a difficult notion for you? Would you comment on some other surface catalysis or electrochemical experiment without knowing anything about it? Why do you accuse me of being a crank or a believer in the Illuminati because I suggest you read papers in the Jap. J. of Applied Physics, Fusion Technology or J. Electroanal. Chem.? These are not fringe publications. They have published 1,200 peer-reviewed papers on cold fusion. If you don't believe that, go to the library and look them up. The papers in my collection came the libraries at Los Alamos and Georgia Tech. These are not fringe institutions.

I urge you to stop ridiculing the work of distinguished professional scientists, and stop pontification about experiments you know nothing about. Your comments are unbecoming. Ridicule and closed-minded dismissal of experimental evidence are unscientific and a violation of academic ethics and traditions. You should be ashamed of yourselves.

Jed, either put or shut up. Either do or fund the experiments, or go away. Welcome to science. I'm speaking as a 30+ year PhD. practitioner of science. Your nagging on the issue is unscientific.

Oh, and Jed, no reputable scientist believes in cold fusion these days. It is considered junk science. So you will need to fund or do the experiments. You might be able to find someone with tenure to run a few expensive experiments for you. One of the original cold fusions scientists went to Japan. Nothing of interest has been heard on the topic since. So put up or shut up, but leave us alone.

Nerd wrote:

"Oh, and Jed, no reputable scientist believes in cold fusion these days. It is considered junk science."

This is incorrect. At LENR-CANR.org you will find hundreds of papers by reputable scientists who believe in cold fusion. They include, for example, two Nobel laureates in physics, the editors of two plasma physics journals and a physics journal; the chairman of the Atomic Energy Commission of India, a Commissioner of the French Atomic Energy Commission; a Distinguished Fellow of China Lake, a Fellow of the Royal Society, hundreds of senior professors and researcher at National Laboratories in the U.S., Italy and China; senior researchers at Mitsubishi, Amoco and Shell Oil, and many other.

This is not debatable. These people have written papers, and you will find them at LENR-CANR.org, or in any university library. It is conceivable that all of these people are wrong, but it is a matter of fact that they wrote these papers. Anyone can confirm this, and you make yourself look foolish denying it.

"Jed, either put or shut up. Either do or fund the experiments, or go away."

As I mentioned, these experiments cost hundreds of thousands to millions of dollars, and they can only be performed in well-equipped corporate and university labs. I am not wealthy, and I am not authorized to allow experiments in university labs. This sort of funding has to come from government agencies and the like. Cold fusion is funding in Italy and China, and by DARPA in the U.S. I think it deserves more funding. You, apparently, do not think so, but based on your other statements about the subject it is clear that you know nothing about it, so you have no right to any opinion.

"Welcome to science. I'm speaking as a 30+ year PhD. practitioner of science. Your nagging on the issue is unscientific."

You may be a 30+ year PhD, but you are not a scientist. A scientist never makes assertions about experiments without first reading the experimental literature. He never denigrates the work of his professional colleagues without even knowing who they are or what they have done. Calling yourself a scientist and getting a PhD does not make a you a scientist. You have to follow the rules, and the first rule of science is to LOOK AT THE DATA. If you judge this experiment -- or any experiment -- without looking carefully at the data then you are not a "practitioner of science." You are practicing a debased form of religion, or science by ESP and Ouija board, in which you make wild guesses about subjects you know nothing about.

Jed, cold fusion is currently a scientific pariah, a fact that you cannot change by hijacking this thread, especially when you attack people for not reading the literature -- those not in the field and not particularly interested in it will go with the prevailing view; they will not spend their time reading papers -- it's a fact of human psychology. Nerd's hostility and hyperbole is unwarranted, but you're unlikely to convince anyone of that. Regardless of experimental results showing excess heat, unless and until cold fusion researchers are able provide convincing evidence of low energy nuclear reactions and are able to provide a plausible physical mechanism, your field will remain in the scientific dog house. In the end, science is a human enterprise and is subject to human social pressures -- read Kuhn.

Jed, in your very first post:

Cold fusion was a debacle. It was replicated in hundreds of labs

Aside from the omission of "not", claiming that it was replicated, and then going on to defend it by pointing to all those papers missed the mark, which was PZ's statement:

science by press release raises my hackles, and has done so ever since the cold fusion debacle.

Regardless of whether it was a debacle, regardless of whether cold fusion is junk science, it is simply false that it was science by press release: Fleischmann and Pons submitted their paper two weeks before their press release. That's what matters here -- not whether cold fusion has been replicated or whether it's like polywater, simply that PZ's concern about this genome announcement being "science by press release" is based on a faulty account of history.

Jed, cold fusion is considered junk science. Period, end of story. Get over it. Either fund or do the experiments yourself (put up), or go away (shut up). Those options are what men of integrity would would do. Your continued posts on the subject would be from a man with no integrity (a crank), will be considered harassment, and given PZ's past history, lead to you being plonked for stupidity.
Now sir, do us a favor and go away.

Nothing wrote:

"Regardless of experimental results showing excess heat, unless and until cold fusion researchers are able provide convincing evidence of low energy nuclear reactions and are able to provide a plausible physical mechanism . . ."

The scientific method does not demand that they provide a plausible physical mechanism. Countless other experimental phenomena have been discovered which could not be explained (at first), but none was rejected for that reason. High temperature superconducting is a recent example. Before that, there was the maser, fission, radioactivity and the x-ray. The Curies discovered radium and were awarded a Nobel long before it was explained.

The test of an experimental effect is whether it can be widely replicated at a high s/n ratio, not whether it can be explained. Cold fusion has met this test. If we reject unexplained anomalies simply because they are unexplained, progress in science will stop.

". . . those not in the field and not particularly interested in it will go with the prevailing view; they will not spend their time reading papers -- it's a fact of human psychology . . ."

That is understandable, and acceptable of course. What is not acceptable if for such people to form an opinion about the research, or to declare the the papers do not exist, or that the researchers are pariahs. People who do not choose to learn about something should not form an opinion about it, positive or negative. That is fundamental to the academic method and the scientific method which is derived from it.

The scientific method does not demand that they provide a plausible physical mechanism.

I'm not talking about the scientific method, I'm talking about how people behave. I'm quite sure I was clear about that.

What is not acceptable

It doesn't matter if it's "not acceptable", it's going to happen.

People who do not choose to learn about something should not form an opinion about it

"should" is an expression of your wishes -- wishes that won't come true.

Jed, Crank and idiot. Go away. Cold fusion is dead. Deal with it.

Nerd wrote:

"Jed, Crank and idiot. Go away. Cold fusion is dead. Deal with it."

You sound upset. Perhaps you are suffering from cognitive dissonance. Do you always react so violently toward calorimetry, mass spectroscopy and x-ray studies? It is odd that you find these subjects so emotionally charged.

Jed, you have nothing to offer but junk science. Go away. Go fund or do your own experiments like a man of integrity. Otherwise you are a CRANK. And you are proving it.

The scientific method does not demand that they provide a plausible physical mechanism.

Jed is a crackpot, a True Believer in a lunatic fringe group. If you step back, they can be amusing for whole minutes. But it is almost impossible to turn a crank.

There is a whole subculture of Infinite Energy people who routinely talk about zero point energy, perpetual motion machines, and cold fusion as if they were real. You can subscribe to their journals and buy their devices on line.

Here is real science for you. "Extraordinary claims require extraordinary proof." Cold fusion has had decades to prove their case. They haven't done so. In fact, the closer people look, the less evidence there is. When making extraordinary claims, the burden of proof is for the claim, not the critics.

I would be the first to change my mind if they had presented evidence. And line up at Walmart to buy a Chinese made Cold Fusion reactor. Isn't happening.

Science doesn't demand a mechanism to explain an observation. But it is strong corroborating evidence absent in a field with no strong observational evidence. 0 + 0 = 0

Raven wrote:

"Jed is a crackpot, a True Believer in a lunatic fringe group."

It is, at least, a large and distinguished lunatic fringe, with hundreds of professors, Nobel laureates, high government officials and so on, as I noted. Very staid.

As I see it, people who attack experimental findings without knowing anything about them are crackpots. Whereas we are, as Martin Fleischmann puts it, painfully conventional people. But everyone has his own set of standards.

"Here is real science for you. 'Extraordinary claims require extraordinary proof.'"

Actually that is TV pop culture, not real science. It is a quote from Carl Sagan Cosmos television series. I enjoyed that show, but that particular assertion has no place in a serious discussion. Extraordinary claims require conventional proof based on standard off-the-shelf instruments and established laws. So do ordinary claims. All claims must be held to the same standards of rigor, including claims by people like you that thousands of experts in calorimetry, x-ray detection and the like have published peer-reviewed papers in major journals but every single one of them is wrong. That is an extraordinary claim! It is, in fact, preposterous. Nothing like that has ever happened in the history of science.

"Cold fusion has had decades to prove their case. They haven't done so."

Yes, they have. You and others repeatedly wave your hands and say that they have not, but denying facts and refusing to look at data does not make the data go away. No skeptic has ever published a peer-reviewed paper showing errors in the major cold fusion studies. Therefore you are wrong. A negative view does not get a free pass. You have to actually prove your point. You have to show why x-ray film and tritium detectors do not work. You have to prove that the laws of thermodynamics are wrong, and calorimeters do not work. The burden of proof on your side is far higher than on ours, and you have not published a single credible paper to support your side, whereas cold fusion researchers have published thousands of papers.

Anyway, I have made my point in some detail. I invite readers to see the actual scientific papers and make up their own minds. I will let you have the last word, which I predict will be a reiteration of: DON'T LOOK. DON'T READ. CRACKPOTS, CRACKPOTS, CRANKS! NEVER READ PEER-REVIEWED SCIENCE! DON'T THINK FOR YOURSELF! NEVER READ ORIGINAL SOURCES! STOP DOING ORIGINAL RESEARCH! IGNORE ANOMALIES! Traditionally, this was considered an anti-intellectual, anti-scientific point of view, more akin to creationism than science, but nowadays it is surprisingly widespread, even among people with 30-year PhDs.

Jed,

If you came to say something, you have said it and can go away. Bye

If you came to convince us of cold fusion, you are wasting your time and ours. We see cold fusion a junk science, and nothing you say will make any difference. So you should move on to find greener pastures. Bye

If you came to make us see the evidence, or talk about it with you, and continue your idiotic posts, you will be plonked as a stupid troll. Bye

By the way, I am a PhD. chemist with 30+ years experience. You can't BS me. BYE

In fact, the closer people look, the less evidence there is.

Not only isn't that true, it isn't logically possible.

When making extraordinary claims, the burden of proof is for the claim, not the critics.

The burden of proof is always on the one making a claim, including when critics make claims.

I would be the first to change my mind if they had presented evidence.

That's absurd -- the cold fusion researchers claim to have presented evidence in their papers, which Jed correctly notes none of us have read.

I don't know if cold fusion is possible -- it seems quite implausible to me. To think that it isn't possible just because it isn't available at WalMart and I haven't personally taken the time to read the literature would be incredibly foolish. I have at least taken the time to read
http://en.wikipedia.org/wiki/Cold_fusion to find out what the current status is, which is very different from what you imagine.

But again, as a matter of the reality of human social pressures, no one will read that, no one will believe Jed, and everyone will align with the herd. C'est la vie.

Traditionally, this was considered an anti-intellectual, anti-scientific point of view, more akin to creationism than science, but nowadays it is surprisingly widespread, even among people with 30-year PhDs.

False dichotomy. It still is considered an anti-intellectual, anti-scientific point of view by rational and honest persons, and it has always been widespread, even among people with academic credentials. Like I said, read Kuhn.

I don't know if anyone is still following this thread, but I had an observation that actually relates to the original topic.

Many of these comments presume the extinction of Neandert(h)al was due to its lack of fitness relative to us, and therefore nothing to get too excited about--a bit sad, perhaps, but just the way life works. Yet I suspect most of the posters would hesitate to say the same of mountain gorillas, or African elephants, or polar bears, or any of the other animals human activities are driving to extinction.

If anatomically modern humans wiped out the Neandert(h)al, maybe the question isn't "What was wrong with them?" but rather, what is wrong with us, that we seem incapable of refraining from genocide, then or now.

This is probably an old idea from the study of myth, but I wonder if the Cain/Abel story could be related to the wiping out of Neandertals.

Obviously, a facile conceit, but it could make for a fun background to an interesting storyline. Maybe it's already been done.

I promise not to get into any more tit for tat disputes, but Nothing's Sacred made some interesting remarks that deserve a response:

"But again, as a matter of the reality of human social pressures, no one will read that, no one will believe Jed, and everyone will align with the herd. C'est la vie."

Actually, a surprising number people are willing to look at cold fusion. We have had 1.6 million visitors at LENR-CANR.org since 2002, and they have downloaded 1.2 million papers. I can tell that most readers are scientists and engineers because readers communicate from time to time (mainly asking for papers not on file), and because these are boring technical papers that ordinary members of the public have no interest in. 1.2 million is nothing compared to web sites devoted to popular singers, but for a technical site it is substantial.

"False dichotomy. It still is considered an anti-intellectual, anti-scientific point of view by rational and honest persons, and it has always been widespread, even among people with academic credentials. Like I said, read Kuhn."

I have read Kuhn, naturally. He makes valid points, but he does social science, not hard science, so it is subject to change and variation. What he describes is more prevalent in some situations and some eras than in others. Here is where it gets interesting! Most cold fusion researchers are elderly scientists, mainly from the WWII and post-war era. (Most of them are retired or dead.) Several of them were at Los Alamos during the war, including the fellow who pushed the button to trigger the first bomb. They saw enormous changes in physics, and compared to modern physicists they were more oriented to experimental science and empirical methods. See Schwinger’s papers at LENR-CANR.org for example.

Compared to scientists under 50, older scientists less conservative, more open minded, pragmatic, empirical (as I said) and more willing to believe that radical new discoveries are possible. Not just in science but in politics and other fields. They have the "Greatest Generation" gung-ho attitude. Freeman Dyson wrote: ". . . [The] experiences of World War II made an indelible impression on people of my generation. At the bottom of our hearts we still believe you can have anything you want in five years if you need it badly enough and if you are prepared to slog your way through the barriers of confusion and incompetence to get it . . . The accepted wisdom says that, no matter what we decide to do about economic problems, we cannot expect to see any substantial results [for 15 years]. The accepted wisdom is no doubt correct, if we continue to play the game by the rules of today. But anyone who lived through World War II knows that the rules can be changed very fast when the necessity arises."

The dispute over cold fusion is split sharply on generational lines. The researchers, who number roughly 2,000 worldwide, are all in their 70s and 80s -- none under 50. I know several of the influential people who lead the opposition to cold fusion at the Washington Post, Time magazine, Sci. Am., the DoE, the APS and the U.S. Congress (Rep. Miller). They are mostly under 50. (The split is also by profession: most of the leading members of the opposition are journalists and politicians without scientific backgrounds. I have spoken with many of these people, and they all tell me they have not read any papers on cold fusion. The editor of Sci. Am. actually bragged to me that "reading papers is not my job"!)

Kuhn’s observations are more true of the modern generation, because -- in my opinion -- basic science and technology has been in stasis since the mid-1950s. Few important new technologies have been discovered since then. We have refined and incrementally improved older discoveries such as jet aircraft, rockets, computers, transistors, lasers and DNA. Very few radically new things have been discovered. This is partly because funding for fundamental research has been cut back drastically since the postwar era; academic freedom has been curtailed; and Washington micromanages research. Tremendous dollar amounts are spent, but they are mainly on absurdities such as Star Wars. The main cause of stasis is that the normal academic opposition to new discoveries and the problems Kuhn describes have intensified. In short, we are living through a fallow, uncreative era in science. No doubt things will recover someday.

Jed, if you want cold fusion worked on, fund it and/or do it. The last meeting to study the issue indicated that DOE should fund well designed experiments in it, but not anything else. (see Wiki article on cold fusion.) So submit a grant to DOE. But first, make it a well designed experiment that will answer questions instead of creating more. Now, get cracking on your grant application, and leave us alone.

If you are interested in the DoE reviews from 1989 and 2004, I suggest you read original sources rather than the Wikipedia summary. See:

http://www.lenr-canr.org/Collections/DoeReview.htm

Wikipedia is inaccurate and biased, in my opinion.

Jed, nobody is interested except you. Stephen Chu is the head of DOE, and he is the one you need to convince, not us. Until you can show the repeatable experiments where the heat is consistently matched by the neutrons given off, I will remain an unbeliever, the same as when I first heard the announcement twenty years ago. Now, you need to convince DOE, who can fund experiments, not us. Go away. If you post again, I will write to Chu, and encourage other here to do the same, telling him that under no circumstances should he fund cold fusion experiments, since they are a waste of the taxpayers monies.

Actually, a surprising number people are willing to look at cold fusion.

I was talking specifically about the dynamics of this site, which reflect the same social pressures that have resulted in cold fusion being a pariah in the scientific community.

Wikipedia is inaccurate and biased, in my opinion.

Of course, but far less so than raven, to whom I recommended it.

You wrote:

"I was talking specifically about the dynamics of this site, which reflect the same social pressures that have resulted in cold fusion being a pariah in the scientific community."

Ah, yes. Good point! It is a sort of microcosm of the larger scientific community. But as you see there is a degree of open mindedness here. The social forces Kuhn described can be overcome, although never easily or quickly. You wrote in a bit of hyperbole: "everyone will align with the herd." Not quite everyone! Not always. If that were true, progress really would grind to a halt and nothing new would be admitted into the canon of science.

I think even the most ardent supporter of cold fusion will acknowledge that the forces Kuhn describes serve a healthy, necessary function. They keep scientists from spinning their wheels and chasing after ephemeral reports of anomalies. There is no harm in ignoring anomalies that are not your job to study, or assuming that incredible reports are probably wrong. Moderation and humility in face of nature are called for.

Jed, either present the evidence for the perfect experiment or go away. I will start composing my letter to Stephen Chu recommending that no cold fusion experiments be funded. It will not be sent if you disappear.

An open mind is important for new ideas to succeed!
Yes Cold Fusion has it's issues but I have heard of some new progress is being made with a process called SuperWave Fusion... Using an interaction between palladium and deuterium they have reported an excess heat reaction. I also read 2 independent labs have replicated the results and the NRL is involved.
I would like to know what others here think.

An open mind is important for new ideas to succeed!
Yes Cold Fusion has it's issues but I have heard of some new progress is being made with a process called SuperWave Fusion... Using an interaction between palladium and deuterium they have reported an excess heat reaction. I also read 2 independent labs have replicated the results and the NRL is involved.
I would like to know what others here think.

Until cold fusion shows the perfect experiment it will remain junk science. Possiblities after twenty years is for get rich quick scheme suckers. One born every minute, but they don't post here.

newideas@99,
Give us a reference or at least a link! Come on, you're asking what we think, at least point us to what you want an opinion on.

I didn't think it would be correct to provide a link
superwavefusion.com