Virus DNA as evidence for common ancestry

Carl Zimmer writes about how retroviruses have inserted themselves into the human genome:

Scientists can identify viruses lurking in our genome (known as endogenous retroviruses) by their distinctive DNA. A fully-functioning retrovirus sequence contains three genes--one for copying DNA, one for a shell, and one for escaping and invading cells. These genes are flanked by a series of repeating DNA, which allow viruses to be inserted or snipped out of their host's genome. The human genome carries full-fledged retroviruses, as well as viruses in various state of decay. Scientists have identified 98,000 of these viruses, along with about 150,000 fragments of defunct viruses. All told, they make up 8 percent of the human genome. In many cases, the virus genes have disappeared altogether, leaving behind flanking repeats, which have been duplicated to millions of copies that take up about 40 percent of the genome. As a point of comparison, our "own" genes--in other words, those that encode proteins that make up our bodies and allow our bodies live--make up only about one percent of the genome.

Some of these endogenous retroviruses are only found in some people and not others. They must have invaded someone's genome and then spread to his or her descendants, but have not yet spread throug our entire species. Others appear to be ubiquitous--meaning that they are ancient passengers that had already spread throughout an ancestral population.

The viruses themselves can change over time, leading to different variants in different individuals that can be compared to reconstruct the lineage of the virus, and reconstruct the older versions of the virus (as was done with the 1918 influenza virus).

Unfortunately for creationists, this also works across species--and human beings share retroviruses in their genome with chimpanzees, macaques, and other primates. Zimmer again:

It turns out that most of the viruses we carry can also be found in these other species. Our retroviruses can be grouped into families. They carry the same families. Our retroviruses usually appear in the same position in the genome, no matter whose genome you look at. Many of theirs are in the same place. These are all the sorts of evidence you'd expect if retroviruses had been carried down from distant primate ancestors. A particular retrovirus is not identical from one host primate to the next, but you wouldn't expect that. Once each host lineage branched off, the viruses could acquire mutations. But the different versions of these retroviruses are still similar enough that scientists can reconstruct the DNA of original virus that infected some long-gone primate.

I recommend reading Zimmer's entire article, "The Sixty-Million-Year Virus," as well as Doug Theobald's "29+ Evidences for Macroevolution: the Scientific Case for Common Descent" FAQ at the talkorigins.org website (the evidence of endogenous retroviruses is item #5 in Part 4 of the FAQ).

Anybody who denies common ancestry of life on this planet does so only by disregarding the evidence.

Misleading commentary on taxes from the Goldwater Institute

On April 3, the Goldwater Institute released a short opinion piece by former state senator Tom Patterson titled "Same Old Story," in which he claims that "A new report shatters the 'tax cuts for the wealthy' myth." But the figures he gives do not shatter any such myth, and the facts are that Bush's tax cuts have gone overwhelmingly to the top 1% of income earners.

Patterson writes:

According to the Congressional Budget Office, between 1979 and 2003 the share of income taxes paid by the highest earning 20 percent of Americans jumped from 65 percent to 85 percent. The top 10 percent of income earners in 2003 paid 70 percent of the income tax. The infamous top one percent shouldered 35 percent of total income taxes paid.
Meanwhile, the proportion of income tax paid by the lowest two quintiles has dropped to minus two percent. And, according to Office of Management and Budget figures, anti-poverty programs in 2004 consumed 16 percent of federal spending, an all-time high.

The first thing to notice about these figures is that the only comparison between two time periods for share of income taxes is for the top 20% of Americans (their share went from 65% to 85% between 1979 and 2003). All of the other figures are for 2003 (except for the 2004 OMB figures on federal spending, which I won't address--I'm just interested in the tax question here).

These figures don't even attempt to refute the claim that the Bush tax cuts primarily went to the wealthiest Americans--this data in no way "shatters the myth." A look at the facts shows that this is no myth.

I sent the following email to Tom Patterson on April 3:

Tom:

This data doesn't seem consistent with other reports of more recent CBO data, e.g.:

http://www.washingtonpost.com/wp-dyn/articles/A61178-2004Aug12.html

It also doesn't seem consistent with the data in David Cay Johnston's book, Perfectly Legal.

Does Riedl look at tax as a percentage of income, as well as just percentage of the tax burden?

My understanding is that tax as a percentage of income has increased on the middle class and bottom of the upper class, while it has significantly decreased for the richest of the rich.

I then included the text of my Amazon.com review of Johnston's book (which I've moved to the bottom of this post). I was mistaken that the facts "aren't consistent" with the other sources--those facts are indeed consistent, but conceals the point that the per-dollar burden on the top 20% has declined. The top 20% is paying a greater share of income tax because they are taking home a greater share of the total income, and being taxed less per dollar of income--and most of that is occurring within the top 10%.

As Johnston's book shows (p. 31), the top 10% of American taxpayers saw their average income rise 88.6% between 1970 to 2000, from $119,249 to $224,877 (inflation-adjusted); their percentage of the total U.S. income increased from 33% to 48%. The bottom 90% of American taxpayers saw their average income go from $27,060 in 1970 to $27,035 in 2000, and their percentage of total U.S. income dropped from 67% to 52%. Within the top 10%, those at the 90-95th percentile saw a 29.6% increase in income between 1970 and 2006, those from the 95th to 99th percentile saw a 54.2% increase in income during that period, those from the 99th to 99.5th percentile saw an 89.5% increase in income, and those in the 99.5th to 99.9th percentile saw a 144.8% increase in income (p. 34). Those in the 100th percentile saw a 558.3% increase in income from 1970 to 2000 (p. 36).

The result of Bush's 2001, 2002, and 2003 tax cuts by 2010 will be an increase in the share of taxes paid by the bottom 95% of taxpayers by 3.8%, and decrease the share of taxes paid by the top 5% by 3.8%. The top 1% will see a decrease in their share by 2.7% (p. 94).
Looking at it another way, the percentage of income paid as taxes by the top 20% of taxpayers in 2001 was 19%; the percentage of income paid as taxes by the bottom 20% of taxpayers was 18% (also p. 94). That's practically a flat tax today, yet the relative burden on the poorest is much greater than on the richest, since a smaller percentage of their income is discretionary.

Dr. Patterson kindly replied to my email:

Mr. Lippard, I appreciate your reply. You bring up a number of interesting considerations, but my column was only a rebuttal of the "Bush tax cuts for the rich hurt the poor" mantra. I think the numbers, while always debatable, are reasonably authoritative and on point, or at least on the point I was trying to make. Tom

If that was what he was rebutting, I didn't get that from the wording--the specific claim made is that the claim that Bush's tax cuts went primarily to the rich is a "myth," and that's just not so.

On April 5, the New York Times reported that:

* Among taxpayers with incomes greater than $10 million, the amount by which their investment tax bill was reduced averaged about $500,000 in 2003, and total tax savings, which included the two Bush tax cuts on compensation, nearly doubled, to slightly more than $1 million.

* These taxpayers, whose average income was $26 million, paid about the same share of their income in income taxes as those making $200,000 to $500,000 because of the lowered rates on investment income.

...

Because of the tax cuts, even the merely rich, making hundreds of thousands of dollars a year, are falling behind the very wealthiest, particularly because another provision, the alternative minimum tax, now costs many of them thousands and even tens of thousands of dollars a year in lost deductions.

And on April 14, Paul Krugman pointed out how the Bush administration has tried to falsely imply that the poor and middle class gained the most from his tax cuts by not being forthright about the actual numbers:

The Treasury Department has put out an exercise in spin called the "Tax Relief Kit," which tries to create the impression that most of the tax cuts went to low- and middle-income families. Conspicuously missing from the document are any actual numbers about how the tax cuts were distributed among different income classes. Yet Treasury analysts have calculated those numbers, and there's enough information in the "kit" to figure out what they discovered.

An explanation of how to extract the administration's estimates of the distribution of tax cuts from the "Tax Relief Kit" is here. Here's the bottom line: about 32 percent of the tax cuts went to the richest 1 percent of Americans, people whose income this year will be at least $341,773. About 53 percent of the tax cuts went to the top 10 percent of the population. Remember, these are the administration's own numbers--numbers that it refuses to release to the public.

Now, it is a simple consequence of mathematics that a government that consumes the amount of tax revenue that the United States does has no choice but to generate most of those revenues from the non-poor, and conversely that the non-poor will get most of the benefits of any tax cuts since they pay the most in taxes. But what the above facts show (and what Johnston's book in particular shows in numerous outrageous details) is that the tax system has been set up in ways that allow the very richest of the rich to benefit even out of proportion to their income, and that the Bush administration has been deceptive about that.

It's high time for real tax reform that greatly simplifies the system, eliminates most deductions and loopholes, doesn't give special breaks for particular corporations owned by friends of people in government, and eliminates the Alternative Minimum Tax. Reducing taxes on dividends and eliminating the estate tax are changes that only benefit the extremely wealthy and don't produce benefits that are likely to create jobs or otherwise benefit most of the population. Reducing taxes on payroll and on small businesses (along with regulatory burdens on them) and eliminating corporate welfare would bring us closer to an actually free market that benefits everyone.

Here's my Amazon.com review of Johnston's book:

While I found much to dismay and horrify me within this book, I suspect I also often did not interpret things in the way the author intended. The author seems to hold a viewpoint in which if you avoid paying a tax--even legally--you have gained income, rather than merely avoided an expense. The author seems to hold the view there is a fixed amount of tax that is the right amount to [be] collected, and if one person or entity reduces its tax burden, it thereby increases the burden on everyone else, cheating them. This is a judgment without any regard to the other side of the coin, government spending. While I agree that at the extremes (many of which are portrayed in this book), there is clear-cut cheating and not paying a fair share by any reasonable standard, I would not agree that all or even most legal tax avoidance falls into that category. Those who favor limited government and balanced budgets are likely to have a similar reaction to much of what the author writes.

That said, however, he makes a very strong case that the U.S. tax system is unfair and corrupt, that the IRS is limited in its ability to go after tax cheats who are breaking the law, and that the net effect is to give tremendous benefits to the richest of the rich, while the burden on everyone else (regardless of whether those taxes are being collected for legitimate or frivolous purposes) has increased.

He has chapters on how the alternative minimum tax (AMT) is completely broken and is now impacting a growing number of the middle class, how tax-exempt insurance companies are being exploited as a mechanism for storing hundreds of millions of dollars in investments and avoiding taxes on the gains, on those who simply refuse to file or pay income taxes at all, on the effects of Reagan-era payroll tax increases, on tax-evading partnership schemes and the IRS's complete inability to devote any resources to detecting them, on American companies moving their headquarters to Bermuda to avoid taxes, and on the destruction of pensions at many large companies. All are fascinating reading.

I agree with the author that something should be done, and that something should include a complete overhaul and simplification of the U.S. tax code, to make it fair and enforceable. But I am not optimistic that anything will be done--I think the level of corruption in the federal government is so high, and that because the behavior of bureaucrats and legislators is more accurately described by public choice theory than by political science, that it is unlikely we'll see radical change in a positive direction.

"Bioprinting": Inkjet printers that build tissue

From New Scientist:

Other tissue engineers have tried printing 3D structures, using modified ink-jet printers which spray cells suspended in liquid. Now Forgacs and a company called Sciperio have developed a device with printing heads that extrude clumps of cells mechanically so that they emerge one by one from a micropipette. This results in a higher density of cells in the final printed structure, meaning that an authentic tissue structure can be created faster.

Cells seem to survive the printing process well. When layers of chicken heart cells were printed they quickly begin behaving as they would in a real organ. "After 19 hours or so, the whole structure starts to beat in a synchronous manner," says Forgacs.

Most tissue engineers trying to build 3D structures start with a scaffold of the desired shape, which they seed with cells and grow for weeks in the lab. This is how Anthony Atala of Wake Forest University and his colleagues grew the bladders which he successfully implanted into seven people. But if tissue engineering goes mainstream, faster and cheaper methods will be a boon. "Bioprinting is the way to go," says Vladimir Mironov, a tissue engineer at the Medical University of South Carolina in Charleston.

(Via jwz's blog.)

Some of the real victims of phony Satanic ritual abuse claims are now seeking compensation

Some of the children who were browbeaten into making admissions of bogus Satanic ritual abuse claims, now adults, are seeking compensation from the government agencies which took them from their families. It's too bad they aren't also going after some of the fakes whose stories inspired the witchhunts (Mike Warnke, "Lauren Stratford," "Rebecca Brown") and their publishers and promoters (Jack Chick, Hal Lindsey, Johanna Michaelsen).

Bush's imperial powers

Scott McClellan maintains that when Bush presented discredited information about mobile bioweapons laboratories in Iraq, he had no choice because the discrediting data was classified and it would be inappropriate to make use of it to modify a set of talking points to make sure that it wasn't full of falsehoods and misrepresentations to present to the American public:

I think the CIA will tell you -- and I spoke to them earlier today -- that a finished product like this, a white paper like this, takes coordination, it takes debating, it takes vetting, and it's not something that they will tell you turns on a dime. It's a complex intelligence white paper and it's ... one derived from highly classified information takes a substantial amount of time to coordinate and to run through a declassification process. And they will tell you this. And the intelligence comes in many different forms -- human intelligence, signals intelligence, open source -- and it's not a trickle, it's a constant flood, is what they told me this morning. And weighing and assessing it is something that takes a lot of time and is a technology-intensive process. So you're making an assumption that something is immediately taken and assessed by your comments.

Yet at the same time, the Bush administration takes such a cavalier view of the declassification process (or rather, such a strong view of the power of the President to act upon the whims of the moment) that he can approve leaking the identity of an undercover CIA agent in order to get revenge on a U.S. Ambassador who is criticizing the administrations falsehoods about Iraq attempting to purchase uranium in Niger.

Meanwhile, Alberto Gonzales says that the President could legally intercept domestic communications without FISA Court approval as a result of the AUMF (authorization for the use of military force in Iraq), in addition to being able to unilaterally declare U.S. citizens to be enemy combatants and hold them indefinitely without trial and engage in torture.

It is growing more and more clear that the current administration thinks the President's powers are unlimited, and Bush's December 18, 2000 comment that "if this were a dictatorship, it would be a heck of a lot easier--so long as I'm the dictator" and his July 30, 2001 Business Week comment that "A dictatorship would be a heck of a lot easier, there's no question about it" weren't really jokes.

Brit accused of killing wife, baby pleads not guilty

The Arizona Republic reports on a tragic situation with a humorously ambiguous headline. This will likely show up in a future issue of Fortean Times.

New Hampshire election phone-jamming tied to White House and Republican Party

An Associated Press story:

Key figures in a phone-jamming scheme designed to keep New Hampshire Democrats from voting in 2002 had regular contact with the White House and Republican Party as the plan was unfolding, phone records introduced in criminal court show.

The records show that Bush campaign operative James Tobin, who recently was convicted in the case, made two dozen calls to the White House within a three-day period around Election Day 2002 as the phone jamming operation was finalized, carried out and then abruptly shut down.

The national Republican Party, which paid millions in legal bills to defend Tobin, says the contacts involved routine election business and that it was "preposterous" to suggest the calls involved phone jamming.

The scheme involved repeated hang-up calls from a telemarketing firm to the Democratic get-out-the-vote headquarters. The owner of the firm is under indictment for the scheme. Apart from Tobin, there have already been two other convictions in the case.

UPDATE: TPM Muckraker has more details on the calling records that show calls to the White House.

Details of AT&T cooperation with the NSA emerge

Details of AT&T's cooperation with the National Security Agency are beginning to emerge as a result of the Electronic Frontier Foundation's lawsuit against AT&T, as described by Wired:

AT&T provided National Security Agency eavesdroppers with full access to its customers' phone calls, and shunted its customers' internet traffic to data-mining equipment installed in a secret room in its San Francisco switching center, according to a former AT&T worker cooperating in the Electronic Frontier Foundation's lawsuit against the company.

Mark Klein, a retired AT&T communications technician, submitted an affidavit in support of the EFF's lawsuit this week. That class action lawsuit, filed in federal court in San Francisco last January, alleges that AT&T violated federal and state laws by surreptitiously allowing the government to monitor phone and internet communications of AT&T customers without warrants.

On Wednesday, the EFF asked the court to issue an injunction prohibiting AT&T from continuing the alleged wiretapping, and filed a number of documents under seal, including three AT&T documents that purportedly explain how the wiretapping system works.

According to a statement released by Klein's attorney, an NSA agent showed up at the San Francisco switching center in 2002 to interview a management-level technician for a special job. In January 2003, Klein observed a new room being built adjacent to the room housing AT&T's #4ESS switching equipment, which is responsible for routing long distance and international calls.

The account says that AT&T's Internet peering traffic, as well as voice traffic, is being intercepted:

"While doing my job, I learned that fiber optic cables from the secret room were tapping into the Worldnet (AT&T's internet service) circuits by splitting off a portion of the light signal," Klein wrote.

The split circuits included traffic from peering links connecting to other internet backbone providers, meaning that AT&T was also diverting traffic routed from its network to or from other domestic and international providers, according to Klein's statement.

The secret room also included data-mining equipment called a Narus STA 6400, "known to be used particularly by government intelligence agencies because of its ability to sift through large amounts of data looking for preprogrammed targets," according to Klein's statement.

This information goes well beyond what had already been determined about AT&T's gigantic call detail record (CDR) database, Daytona, that preserves a record of decades of telephone calls. That database included only the phone numbers and dates and times, not the actual content of the calls. This new information, by contrast, suggests the ability to actually intercept the content of voice calls and Internet data transmission.

Direct Revenue exposed

The NY AG's lawsuit against Direct Revenue has produced a bunch of interesting internal documents. The documents include complaints, internal emails, a listing of company names used by Direct Revenue, information about Direct Revenue hiring a private investigator to track down an anti-spyware researcher, payments received from Yahoo ($600,000 between April-June 2005), and revenue numbers (the adware business is extremely profitable). Ben Edelman has them up at his site.

Tiktaalik roseae and the Discovery Institute

The Discovery Institute wants to argue that Tiktaalik roseae is not a transitional fossil (images here). Nick Matzke dissects the DI's claims at The Panda's Thumb.