Monthly Archives: February 2010

Pics of Our New (Old) Home

Yesterday, we got busy with the fixing-up of the fixer-upper in Palmetto. While Sam worked on the electrical panel, I made a photographic record of the state of the house. We plan to ask Manatee County for a re-appraisal as the house is currently not ready for occupancy. So I have about 3.5 GB of photos showing everything from the exterior views below to the various fixtures without cover plates.

There was soaking rain when we left Clearwater. By the time we got to Palmetto, that had slowed to the drizzle. About an hour after we arrived, the clouds cleared and we had some sunshine. We took advantage of that to have a bit of a picnic lunch in and just outside the garage. I had called Manatee County during the week about a couple of abandoned vehicles parked on our seven acres, and the towing service sent out two tow trucks to handle those while we were there on Saturday.

The house itself was built in 1955. We’ve been told that it was neglected for some time before its purchase in 1998 by the previous owners. They replaced much of the roof structure and were working on renovating the interior room by room. The floors are all done in tile, with the exception of the hall bathroom and a couple of closets in the hall that are unfinished. The hall bathroom is completely stripped out, with exposed drywall and the previous set of tile taken off. There are no fixtures in there, so part of our work will be to get the hall bathroom finished again. The interior paint job was not complete, so we have that to look forward to as well. There is a bedroom suite at the east end of the house, with two adjoining rooms and a master bathroom. We are contemplating redoing the doorways there to make the rooms separate, rather than simply having a shared door to the hallway.

Because the place was foreclosed, there is essentially nothing more complex than ceiling fans still there, except for the central air conditioning and heating system. We will need to get ourselves an oven/range combo unit, refrigerator, and, eventually, a dishwasher. There’s nothing in the utility room, so we can add getting a washer and dryer as well. It looks like the water heater in the garage is actually relatively recent (the tag references efficiency figures from 2004).

So on with the pictures. The exterior shots don’t hint at the work to be done on the inside.

Wider view from southeast.

Wider view from southeast.

Closer view of south side (front).

Closer view of south side (front).

View from driveway.

View from driveway.

View of west side with garage.

View of west side with garage.

Home, Sweet Home: Florida

We looked at a property last September that stood out as a candidate for a home purchase. It had a house on 7 acres of land, and we could afford the asking price… barely. Now that might be ringing all sorts of bells, and to be sure there is a laundry list of issues to go with the house and the property. But there was nothing else close to it in terms of something that we could afford within commuting distance of downtown St. Petersburg that actually had a livable, or not-too-much-repair-needed-to-make-it-livable, house plus some land so that we had a place to train the dogs in agility or flyball.

The property is in Palmetto, Florida, and runs alongside a railroad line easement. It used to be a strawberry farm, but more recently the former owners had used it as a place to dump lumber from a tree surgeon’s patients and to fix up stock cars. It was foreclosed on last year, so we bought it from the bank. That turned out to be a saga, and took about as long as the usual short sale, despite the fact that we were dealing only with the bank’s selling agent.

You see, we got under contract for the place early in November. But it turned out that the bank’s title was incorrect, something that our lawyer pointed out to us. They had failed to get the easement for ingress and egress recorded when they foreclosed. So their task was to go back to the court and get the title corrected. We thought that our closing could be done late in November, but we got word that the seller’s agent wanted to extend to December 18th. Our real estate agent discouraged us from having any contact with the seller or people working for the seller, so time simply passed by until mid-December, when the seller’s agent again proposed an extension, this time to December 28th.

That got us worried about the process. I went online and found that Manatee County had an excellent online site for their courts. I found out that there was no scheduled motion putting the issue before the court. We gave up on the notion of being passive buyers at that point. Diane got the lead for which law practice was involved in the case and contacted them. It turned out that the first request for a change to the title was incorrectly formed, and the clerk had kicked it back with instructions for correction. In the meantime, the lawyer at the firm handling the case had moved on to other employment, and had not passed on the file to anybody else there. So as far as anybody at the firm could tell, the file needed no action. It took Diane’s pushing to locate someone there who agreed to pick it up and finish the job. But at that point, the holidays were in full swing, and it became apparent that nothing further would be done before the end of the year. With that also ended our anticipation that we could at least camp out in the house as ours in order to claim homestead exemption for 2010. The next extension took us into January, and more interaction with the lawyer handling the title correction effort. But it became apparent that things would not move fast enough to close in January. The next extension put the closing date at February 15th.

The court did act before the end of January, but getting the change recorded took us into early February. At that point, the seller’s agent finally woke up to the fact that the property could be sold, and started pushing for a close as fast as possible. We, though, needed to have the corrected title before ordering a survey, and getting the survey scheduled was an adventure itself. With assistance from the title company, we settled on a closing date of February 24th and worked toward that. The survey team actually got out to the property on the 19th, and the title company got the completed survey yesterday. Today, we got our funding sent to the title company in two wire transfers and went to their office in Tampa to get our papers signed and notarized. About an hour after that, the title company told us that the sellers had signed off on the settlement statement.

We still have oodles of work to accomplish before we can actually move in. But we’ve managed to clear a huge hurdle. The place is ours to restore and make our own.

Rob Crowther, Again

Rob Crowther’s latest post over at the DI’s propaganda page is quite short.

Darwin was wrong.
Missing links still missing.

There is no such thing as junk DNA.
Birds did not descend from Dinosaurs.
Irreducible complexity is still irreducibly complex.
Tiktaalik has been invalidated by an earlier ancestor.

Haeckel’s embryo drawings are still fake (and still in textbooks).

Yet, evolution is a fact?

Yes, Rob, the fact that evolution has occurred is still quite secure.

The link Crowther gives to show “Darwin was wrong” leads to the table of contents for an issue of “New Scientist”, and the editorial in there discusses the probable misuse ignorant charlatans would make of their content:

As we celebrate the 200th anniversary of Darwin’s birth, we await a third revolution that will see biology changed and strengthened. None of this should give succour to creationists, whose blinkered universe is doubtless already buzzing with the news that “New Scientist has announced Darwin was wrong”. Expect to find excerpts ripped out of context and presented as evidence that biologists are deserting the theory of evolution en masse. They are not.

Nor will the new work do anything to diminish the standing of Darwin himself. When it came to gravitation and the laws of motion, Isaac Newton didn’t see the whole picture either, but he remains one of science’s giants. In the same way, Darwin’s ideas will prove influential for decades to come.

So here’s to the impending revolution in biology. Come Darwin’s 300th anniversary there will be even more to celebrate.

So Darwin was wrong kind of like Newton was wrong. Way to shoot yourself in the foot, Rob!

But, really, we in science don’t count Darwin as a prophet, someone who must have provided the whole truth that would stand unaltered until the end of time. Charles Darwin was a scientist, someone who contributed quite a lot to the process of coming to understand things the way they can be tested to be. The article referenced by the editorial and presumably by Crowther as well does not deliver anything like a result that evolution is not a fact. It simply argues that more evolution occurred by horizontal gene transfer than has been generally recognized, and this puts one organizing metaphor Darwin introduced, that of a “tree of life”, at risk. More ways to pass genetic material than from parent to offspring of the same population doesn’t make evolution any less a fact; it just makes it tougher to analyze.

There’s this bit from the New Scientist article that should have given Crowther pause:

Nobody is arguing – yet – that the tree concept has outlived its usefulness in animals and plants. While vertical descent is no longer the only game in town, it is still the best way of explaining how multicellular organisms are related to one another – a tree of 51 per cent, maybe. In that respect, Darwin’s vision has triumphed: he knew nothing of micro-organisms and built his theory on the plants and animals he could see around him.

While I think the last sentence is hyperbolic, it certainly is the case that Darwin’s thinking and lines of evidence were about multicellular plants and animals. Was Darwin wrong in a way that would say anything about human descent from primates? Not according to the New Scientist article linked to by Crowther.

Next… Crowther doesn’t like found links, and points to people urging greater circumspection in describing one particular fossil, “Ida”, as showing that “missing links are still missing”. I agree with the authors of the linked articles that hype is bad and that inaccuracy is bad. But Crowther is somehow thinking that these criticisms support his contention that evolution is not a fact, and it does nothing of the sort. One doesn’t determine the factuality of evolutionary change by negatives; conceptually, if evolutionary change happens even once, evolution is a fact. So Crowther can’t point to something as not qualifying as a particular transitional fossil to get to his desired conclusion; he would have to demonstrate that every single instance of a transitional fossil is somehow wrong. I have no doubt that this is well outside of Crowther’s capabilities. If Crowther insists that there aren’t any transitional fossils at all, I’d be happy to have him take the Transitional Fossil Existence Challenge.

Next… Crowther does claim that there is no “junk” DNA. This is a standard antievolutionary claim, one that is recorded in Mark Isaak’s compendium of creationist claims as CB130.

It has long been known that some noncoding DNA has important functions. (This was known even before the phrase “junk DNA” was coined.) However, there is good evidence that much DNA has no function:

* Sections of DNA can be cut out or replaced with randomized sequences with no apparent effect on the organism (Nóbrega et al. 2004).
* Some sections of DNA are corrupted copies of functional coding DNA, but mutations in them, such as stop codons early in the sequence, show that they cannot have retained the same function as the coding copy.
* The fugu fish has a genome that is about one third as large as its close relatives.
* Mutations in functional regions of DNA show evidence of selection — nonsilent changes occur less often that one would expect by chance. In other sections of DNA, there is no evidence that any changes are selected against.

The article that Crowther links his claim to doesn’t make the case that there isn’t any “junk” DNA, just that researchers have found evidence that particular parts of non-coding DNA do actually have a function in one species. They speculate that much of what is considered non-functional may have function after all, but nowhere does the exclusive claim Crowther makes get support in the linked article. Coupled with the various facts assembled by Isaak above, it looks like Crowther has once again grasped the wrong end of the stick.

Next… Crowther apparently doesn’t like the notion that birds descended from dinosaurs. The linked article does dispute the birds had dinosaurs for ancestors, but says not one word that would dispute the fact that birds descended from reptiles (pardon the non-cladistic usage). How does one get to evolution not being a fact from disputes over a relatively difficult area of phylogenetic inference?

Next… irreducible complexity and Crowther doing some cheerleading for Michael Behe. Crowther’s source for Michael Behe’s notion of irreducible complexity being still a good thing is … Michael Behe. How does citing a tendentious antievolutionist go anywhere near showing that evolution is not true?

Next… Crowther doesn’t like the Tiktaalik fossils. So how does finding tetrapod trace fossils demonstrate that evolution is not a fact, or even that a fossil can be “invalidated”? Crowther failed to learn from the lesson delivered by PZ Myers to Rob’s fellow DI denizen, Casey Luskin. Instead, Rob chose to take on some of that embarrassment himself.

Next… Haeckel’s embryo drawings are a perennial DI talking point, and, predictably, Crowther talks about them. His link goes to a DI-produced YouTube video featuring Jonathan Wells. Wells apparently can’t take on the assessment of even Haeckel’s modern scholarly critic, M.K. Richardson:

On a fundamental level, Haeckel was correct: All vertebrates develop a similar body plan (consisting of notochord, body segments, pharyngeal pouches, and so forth). This shared developmental program reflects shared evolutionary history… Haeckel’s inaccuracies damage his credibility, but they do not invalidate the mass of published evidence for Darwinian evolution. (Richardson et al. 1998, p. 983-984)

What about the claim about textbooks? The National Center for Science Education sheds some light on that:

Explore Evolution repeats another false claim from Wells.

This error even crept into the Encyclopedia Britannica, and remains in many modern high school and college biology textbooks.
Explore Evolution, p. 69

This is incorrect. A recent survey of 36 biology textbooks, dating from 1980 to the present and covering high school biology, college introductory biology, advanced college biology, and developmental biology books, found that only 8 of these textbooks mentioned Haeckel or the biogenetic law. Two of these 8 were creationist/ID books (Of Pandas and People, and Biology for Christian Schools from Bob Jones University Press). Of the 6 mainstream textbooks that mentioned Haeckel or the biogenetic law, two are advanced college-level books. In all cases where Haeckel is mentioned (except for the creationist/ID books), the text discussion does not reproduce Haeckel’s mistakes.

Crowther was wrong yet again… what a surprise.

I don’t know, I didn’t see anything in what Crowther provided that would address whether evolution is a fact, much less that would put the fact of evolution in doubt. Crowther’s post does lend support to the notion that what he writes is not a fact, though.

Luskin on Information: Part 0

Casey Luskin has decided to treat us to an agony in eight fits, wherein he will whine mightily concerning “information”. I don’t know how many of those I’ll be taking note of, but I might as well have a look at the first one.

It does not augur well for the series. Luskin leads with a lot of bluster, claiming that citations to the scientific literature on the topic of genetic information were “bluffs”. It seems dubious to me that Luskin will be able to do more than try to spin armchair philosophy stuff from William Dembski and Stephen Meyer as somehow putting actual research in doubt.

Here’s an example of Luskin innuendo, complete with scare quotes:

Virtually all of those “publications” mentioned by Judge Jones came from one single paper Miller discussed at trial, a review article, co-authored by Manyuan Long of the University of Chicago.4 The article does not even contain the word “information,” much less the phrase “new genetic information.” 5

Well, a publication is still a publication, and a peer-reviewed one to boot, even if it is cited in a review article, so it is unclear what, exactly, Luskin is trying to do with the scare quotes. Usually the Discovery Institute (DI) is all for counting any odd scrap of paper with print on it as a publication, even inventing meaningless phrases like “peer-edited” to try to put some cachet on obvious partisan near-vanity press dreck. Perhaps the DI respect for articles and books only goes so far as to cover those that toe the “intelligent design” creationism (IDC) party line.

One can see that Luskin managed to shoot himself in the foot in that sentence-as-paragraph. Notice the footnote. That goes down to this text:

[5.] The word “information” appears once in the entire article—in the title of note 103. Id. at 875 n. 103. See Manyuan Long, Esther Betrán, Kevin Thornton, and Wen Wang, “The Origin of New Genes: Glimpses from the Young and Old,” Nature Reviews Genetics, Vol. 4:865-875 (November, 2003).

So, Casey, how is it that you can get all huffy about someone not including a specific phrase of “new genetic information” when the title promises that the article is about “new genes”? Do you suppose that “new genes” are never associated with new genetic information? If you were that nit-picky about things being different you wouldn’t have been making those claims about the degree of “near-verbatim” passages in the Kitzmiller decision. It appears that the one trait that runs through both of the aspects of Luskin’s text discussed above is hypocrisy.

It gets worse from there.

But are Judge Jones’s, Ken Miller’s, and the NCSE’s bold proclamations supported? Does Long et al. actually reveal the origin of new biological information? Is Explore Evolution wrong? A closer look shows that the NCSE is equivocating over the meanings of the words “information” and “new,” and that the NCSE’s citations are largely bluffs, revealing little about how new genetic functional information could originate via unguided evolutionary mechanisms. This bluff was accepted at face value by Judge Jones, who incorporated it in his highly misguided legal ruling.

No, Casey, the equivocation about “information” comes from antievolutionists like your colleague William Dembski. As for “new”, this point can be found in the transcript of the Kitzmiller trial, where Scott Minnich was cross-examined by Pepper Hamilton’s Stephen Harvey. When asked about the evolution of a DNT breakdown system that evolved in bacteria, Minnich agreed that the multi-part system developed naturally, but dismissed it as an “adaptive response” rather than being evolution per se. But the IDC mindset comes through clearly there, as Minnich testified:

Q. And if you look on — at figure 1, which is on page 113. And Matt, perhaps if you can bring that up for us. These researchers, based on their own original data, have published the organization and evolution of the bacteria that breaks down DNT?

A. Right. This is an adaptational response.

Q. And that’s a DNT — this process by which these bacteria breakdown DNT, that’s a biochemical pathway?

A. Correct.

Q. So we do have published information in this scientific literature about the evolution of biochemical pathways?

A. Steve, you’re extrapolating from the data here. I mean, not all these enzymes evolved specifically to break down this compound. I mean, you’re mixing and matching enzymes, I’m sure, from pathways that had some other property.

It’s pretty simple, really. A gene is new if it was not there in the population before but is now. A system is new if it does something that was not done before. Evolution, if Luskin had paid attention in class (and I don’t know what excuse Minnich could claim), works by modification of what exists. And sometimes those modifications result in novel functionality.

As for the stuff we don’t see happening in living systems, as alluded to in Minnich’s testimony, the de novo injection of systems that had no precursors, that’s what is known as “special creation”. It’s pretty ironic that when trying to figure out what they want from evolutionary science, quite commonly the antievolutionists are really asking that biologists demonstrate that creationism is observed.

Casey Luskin again:

In fact the origin of new functional biological information is perhaps the most important question in biology. As origin of life theorist Bernd-Olaf Kuppers stated in his book Information and the Origin of Life, “The problem of the origin of life is clearly basically equivalent to the problem of the origin of biological information.”8

Now, I think someone introduced the word “equivocation” into the discussion. Right, that would be Casey. And here we see why Luskin introduced “equivocation” into the discussion: he’s projecting. There’s something a bit different between the processes that we see happening in the evolution of living things (the subject of discussion) and pre-biotic chemistry when talking about new genetic information. That would be that there is a system of inheritance established and operating in living things, something that is not available as an assumed starting position in origin-of-life research. So dropping origin-of-life into the discussion is simply a non sequitur, though one that has strong misleading properties.

Casey Luskin:

Judge Jones was not merely in error. Worse than any simple mistake, the misinformation he propounded in his ruling entered media and academic culture, becoming enshrined as a Darwinian myth, alongside many others. This myth holds that perhaps the most important question in biology has been solved, when really (as this series of 8 total posts will show), that is far from being the case.

This is what the lawyers call “an appeal to facts not in evidence”. In fact, parts of this have already been proven false just in the discussion above, and Luskin hasn’t even gotten around to much more than a quote-mine, some projection, and a double dollop of hypocrisy. Nor do I have any expectation that the parts yet to be published will do any better than Luskin’s initial poor showing.

Refreshing Data Storage

I have data on Compact Disks (CDs) from past projects. The technology was getting toward being affordable around 1996. CD writers dropped under $100 for the first time somewhere around there, and media started selling for less than $5 a disk. The amount of storage space on a CD was comparable to the size of hard disks available at the time, and optical storage seemed far better than tape as a medium. So now I have cases, drawers, and spindles of CDs dating right back to 1996.

No storage medium is perfect, so archived data is a commitment and not just a static collection. Last month, Sam asked me what I would like for my birthday. I said I wanted a disk for backing up data. After having a look at off-the-shelf external hard drives, it seemed that all the models I looked at had warranties of 1 year or shorter. However, if you buy an internal hard disk and a separate USB enclosure, the warranty on the drive can be much, much longer. Sam and I visited the Newegg site and picked out a Western Digital 1.5 terabyte drive and a Rosewill USB enclosure. The drive comes with a 5-year warranty. I can pair this with another 1.5 terabyte disk so that I can copy off my data from the CDs, then copy to the second hard disk.

Back when I was about to move from California to Michigan, I had a chat with a fellow who works for the Internet Archive. That is a project whose modest aim is to store the World Wide Web. All of it. You can browse sites as they were in 1995. Well, with a few caveats. My acquaintance said that the Internet Archive’s data storage was based on consumer-grade IDE drives. You can get them cheap and in quantity, and if you store things on multiple disks, the redundancy will help. That’s because disks fail. With an organization like the Internet Archive, they rack up lots of failures. They have to be swapping out bad drives and attempting to restore content from remaining copies on other drives. And they couldn’t, he said, quite keep up with the failures. Some data does get lost because failures occur before the redundancy can be exploited to restore some sites.

I figure for my purposes, the data I have is a copy of what my colleagues have, and for the hard disk copy, I aim to have two of those. I think that should be sufficiently paranoid. The process or workflow takes about six to seven minutes per CD to create a directory, copy the files, and mark the CD as copied. I’m working on the third page out of 32 pages in a CD case now. This will take some effort, but then I invested years of my life getting that data in the first place.

“Signature in the Cell” Tampa: Part 3

Throughout the evening, Stephen Meyer kept repeating that we only know of “specified information” occurring because of an intelligent agent acting. Then, because we only know one cause in the present for “specified information”, we should accept that as the cause of “specified information” in the past.

Besides the philosophical problems with rarefied design inferences, there is the rather more simple class of empirical counterexamples. To wit, Meyer has consistently ignored available evidence that is not in accord with his outlook. What designer, for example, must be posited as acting in any of the various cases of duplicated genes that diverge and where the copies now each yield different functional protein products? Meyer has been ignoring this despite notice in 2004 of this class of evidence.

“Signature in the Cell” Tampa: Part 2

Michael Medved dismissed accusations that the IDC movement was disguised religion as a “big lie”. Elsewhere in his remarks, he claimed that the vociferousness of the attacks on IDC were because of belief. IDC advocates, Medved claimed, would have no change in their faith if “Darwinian evolution” were proved correct (to the satisfaction of their doubts, certainly), but that atheists would have to admit that they were wrong if IDC proved correct.

OK, so if IDC is correct, how would that change any atheist’s mind about things? It seems to me that’s only the case if one assumes that the “intelligent designer(s)” is/are identical to some conception of God(s). That rather diminishes the force of Medved’s other assertion that IDC isn’t about religion.

Plus, there’s the consideration that Medved overlooks in his dichotomizing. There are rather a large group of us outside the IDC “big tent” who grew up being told that telling the truth was good and telling falsehoods was bad. Maybe the IDC movement gets vociferous opposition because rather a lot of us take umbrage at so many falsehoods being spewed by such a small group? Please, Michael, remember to expand your remarks next time to take us into account.