Chirality and Life

Marcelo Gleiser is, if not more intelligent, certainly more educated than I am. Thus I'm a but surprised to find such fundamental errors of thinking in his latest SEED article, here. Gleiser states, quite correctly, that all the proteins that make up life could, chemically, be right-oriented or left-oriented. He also cites his and colleagues' research that the early Earth appears to have contained molecules of both chiralities, and then asks why life only has left oriented molecules present. Marcelo, how is this not at least semi-obvious?
Let's start with a fundamental assumption; Life began once and only once on our planet, created from (insert correct answer here, we don't have it yet) to form self-replicating strands of nucleic acids and the proteins for which they code, somewhat like viruses or prions. This isn't that poor of an assumption, given the low probablity of spontaneous generation of life in the first place. It had to happen somewhere, given the numbers of stars and planets, and obviously it happened here or we couldn't write and read blogs written by graduate students of no current academic importance, but proposing it occured multiple times is a bit of a mathematical stretch. If you'd like, we can concede that life was unlikely to start more than once at a time, allowing the possibility that early life began several times sequentially, and that will not affect this dicussion at all. So, given that life occured once, or once to start, then the proteins incorporated in that first organism were likely of one chirality, given the simplicity of early life-like molecules and the coding for proteins written into whichever nucleic acid (likely RNA, from current evidence) was employed. That life had to replicate, using the available amino acids, proteins, and other molecules, and would replicate using the same structure without fundamental changes in the RNA (mutations). Molecules of the wrong chirality couldn't even interact chemically with those of early life, it'd be life trying to use the mirror image of a key. (Gleiser uses the mirror analogy to describe chiral molecules first, and it's apt, so I'm stealing it. Thanks Marcelo, you'll never likely see this, but I'm giving credit anyway)
Briefly, then, what we're seeing in the exclusivity of "left-handed" proteins is a what Dawkins calls a frozen accident, the vestige of the structure of our most distant ancestors and the necessary structures for their replication and survival, all the way down to us. There's no reason to suppose that life on other planets would necessarily follow this blueprint, and actually finding samples would be a requirement for making any statements of that kind.

Gleiser states it thusly:

If one traces life’s origins from its earliest stages, it’s hard to see how life began without molecular building blocks that were “chirally pure,” consisting solely of left- or right-handed molecules. Indeed, many models show how chirally pure amino acids may link to form precursors of the first protein-like chains. But what could have selected left-handed over right-handed amino acids? My group’s research suggests that early Earth’s violent environmental upheavals caused many episodes of chiral flip-flopping. The observed left-handedness of terrestrial amino acids is probably a local fluke.

Obviously we're not far apart on most of this view, it's the "it's hard to see how" statement that vexes me... his local fluke may be much more local than he believes, as in local to the particular location on the planet where life began.

Sham Charity...

http://www.orphanage-outreach.org/

An organisation called Orphan Outreach runs volunteer trips to the Dominican Republic, many of which are taken by public schools. This, at first glance, sounds like a wonderful idea. The issue I derive from this is that the founders of O.O. are not only religious (that's immaterial), but that they require the orphans to attend Pentecostal Church services nightly, according to their volunteer guide. Volunteers, of course, aren't mandated to attend, but then again they aren't the target here. On top of that, the volunteers are required to not only pay for the trip ($1600 for a week) and their own airfare, they're expected to bring a 50lb. suitcase of food to donate and give any flight coupons that might be received if they're bumped on a flight. Hmm... not that I have a problem with supporting the orphanage, but if I chose to go and volunteer, what would I have to pay $1600 for a week's worth of beans and rice and a place to sleep under a mosquito net in an open air building? What exactly does that money cover? Not to mention that fact that I would then get to pass through customs in a third world nation with 50lbs of food, and then identify myself as an American for a nice trip through an area where we're advised by the State Department not to travel alone or after dark. It sounds to me like, under the guise of a good cause, those who run this programme are financially exploiting the charitably minded and seeking to convert young children to their religion.

Pat Condell's latest...

Patriotic Jackassery

Someone will disagree with this, but, hell, someone disagrees with everything else I write as well. At the outset of a school pep rally today, our athletic director threw out two male Hispanic students who refused to stand and recite the Pledge of Allegiance. They weren't disruptive or disrespectful, in fact they weren't even speaking, they simply didn't stand and say the pledge. I was told, by the athletic director, to take them to our version of in-school suspension for that "offence", which I refused to do. Rather, I let the students stand just outside the gym doors and watch until I could get the attention of an administrator who promptly took them back in to be seated. The AD is furious that I went over his head (and that I took the students' side on this).
As I explained to the AD, I also refuse to say the pledge, although not for the same reasons as the students. Unless our government sees fit to remove the blatant and unconstitutional endorsement of religion from that document, I will continue to refuse to say the pledge, and if that were to happen I would still have reservations in publicly swearing allegiance to a piece of cloth and the nation. I have no intention of betraying the nation in which I live, and there are a number of things about this country that I admire and support, not least the fact that I have the freedom/right to decide whether or not I wish to say something like the Pledge of Allegiance because of the way our government was constructed. The students actually refused because they aren't yet citizens of the U.S., although they are here legally. That two adolescents (17 and 18 respectively) chose not to swear allegiance to a nation, of which they are not citizens (and that, at times, treats those of their ethnicity rather unjustly, to say the least), does not offend me in the least as a citizen of that nation. The athletic director, on the other hand, was absolutely incensed both with their conduct and my failure to condemn it.
A little research turns up this gem: 1943 West Virginia State Board of Education v. Barnette, in which the Supreme Court ruled that it was unconstitutional for the government, schools included, to compel speech in the manner of the Pledge. This at the height of World War Two, no less. Attempts since then to challenge the constitutionality of the words "under God" in the pledge, as they expressly support monotheism as a religious belief, have not resulted in Supreme Court rulings ( Newdow v. California was dismissed because the plaintiff was deemed not to have parental standing in the case). There are a number of more recent rulings that uphold the opinion that coercion of speech is not constitutional.
Basically, Wake Co. schools should be thanking me for saving them a lawsuit. Somehow I doubt I'll ever hear that thanks.

Teh Stoopid, it Burnz

Warning: This will be lengthy

I received this email a few days ago, forwarded by a childhood friend of mine who is quite intelligent, and , I thought, fairly reasonable and rational. As she's not the author of the illogical piece of trash I'll quote in a moment, I'll reserve any judgement and simply consider that she probably shares the neo-con political views of her parents. Needless to say, I do not, a fact of which she is apparently not aware when forwarding this drivel.

The Truth About the Health
Care Bills - Michael Connelly, Ret. Constitutional Attorney
08.24.09



Well, I have done it! I have read
the entire text of proposed House Bill 3200: The Affordable Health Care
Choices Act of 2009. I studied it with particular emphasis from my area
of expertise, constitutional law. I was frankly concerned that parts of
the proposed law that were being discussed might be unconstitutional.
What I found was far worse than what I had heard or expected.



To begin with, much of what has been said
about the law and its implications is in fact true, despite what the Democrats
and the media are saying. The law does provide for
rationing of health care, particularly where senior citizens and other
classes of citizens are involved, free health care for illegal immigrants,
free abortion services, and probably forced participation in abortions by
members of the medical profession.



The Bill will also eventually force
private insurance companies out of business, and put everyone into a
government run system. All decisions about personal health care will
ultimately be made by federal bureaucrats, and most of them will not be health
care professionals. Hospital admissions, payments to physicians, and
allocations of necessary medical devices will be strictly controlled by the
government.



However, as scary as all of that is, it
just scratches the surface. In fact, I have concluded that this
legislation really has no intention of providing affordable health care
choices. Instead it is a convenient cover for the most massive transfer
of power to the Executive Branch of government that has ever occurred, or even
been contemplated. If this law or a similar one is adopted, major
portions of the Constitution of the United States will effectively have been
destroyed.



The first thing to go will be the
masterfully crafted balance of power between the Executive, Legislative, and
Judicial branches of the U.S. Government. The Congress will be
transferring to the Obama Administration authority in a number of different
areas over the lives of the American people, and the businesses they own.



The irony is that the Congress doesn't
have any authority to legislate in most of those areas to begin
with! I defy anyone to read the text of the U.S. Constitution and find
any authority granted to the members of Congress to regulate health care.



This legislation also provides for
access, by the appointees of the Obama administration, of all of your personal
health care information, your personal financial information, and the
information of your employer, physician, and hospital. All of this is a
direct violation of the specific provisions of the 4th Amendment to the
Constitution protecting against unreasonable searches and seizures. You
can also forget about the right to privacy. That will have been
legislated into oblivion regardless of what the 3rd and 4th Amendments may
provide.



If you decide not to have
health care insurance, or if you have private insurance that is not deemed
acceptable to the Health Choices Administrator appointed by Obama, there will
be a tax imposed on you. It is called a tax instead of a fine because of
the intent to avoid application of the due process clause of the 5th
Amendment. However, that doesn't work because since there is nothing in the
law that allows you to contest or appeal the imposition of the tax,
it is definitely depriving someone of property without the due
process of law.



So, there are three of those pesky
amendments that the far left hate so much, out the original ten in the Bill of
Rights, that are effectively nullified by this law. It doesn't stop
there though.



The 9th Amendment that provides: The
enumeration in the Constitution, of certain rights, shall not be construed to
deny or disparage others retained by the people;



The 10th Amendment states: The powers not
delegated to the United States by the Constitution, nor prohibited by it to
the States, are preserved to the States respectively, or to the people.
Under the provisions of this piece of Congressional handiwork neither the
people nor the states are going to have any rights or powers at all in many
areas that once were theirs to control.



I could write many more pages about this
legislation, but I think you get the idea. This is not about health
care; it is about seizing power and limiting rights. Article 6 of the
Constitution requires the members of both houses of Congress to "be bound by
oath or affirmation to support the Constitution." If I was a member of
Congress I would not be able to vote for this legislation or anything like it,
without feeling I was violating that sacred oath or affirmation. If I
voted for it anyway, I would hope the American people would hold me
accountable.



For those who might doubt the nature of
this threat, I suggest they consult the source, the US Constitution, and Bill
of Rights. There you can see exactly what we are about to have taken from us.



Michael Connelly

Retired attorney,

Constitutional Law Instructor

Carrollton , Texas

Well, there are some issues I can't argue here, since Mr. Connelly wasn't kind enough to actually link the bill itself. For one, I can't imagine how he could be privy to that information being a Constitutional Law instructor at where ever he may be (There are no accredited colleges or universities listed in Carrollton, TX)Since that's an argument from personal ignorance, let's give credit where none is likely due and pass over that issue altogether.
If by rationing of health care the author means that health care will be provided only to those who actually need that care, as determined by a medical professional, he's probably right, and I fail to see a problem with this. I personally don't want to pay for health care that I don't need, nor, I assume, would he. Other nations with nationalised health care actually provide services for everyone who's there, so giving care to "illegal immigrants" is a certainty if we follow working models. There's something rather inhumane about denying someone needed medical services because they talk funny, or were born elsewhere, so I invite you to consider the motives behind the author's complaint. I'd guess he doesn't like brown people much, but that's a bit hasty, we can find that out from further conversation (or could if he'd bothered to allow a way to respond personally to his diatribe). Abortion happens to be legal in this country, courtesy of Roe v. Wade, so the complaint that a new system would fund abortion is likely motivated religiously. Likewise the complaint that health care providers will be forced to provide a legal service to their constituents. "Family Planning" clinics that don't provide abortions, and even fail to refer patients to places who do, aren't all that scarce. Perhaps we can lift the misogyny long enough to correct this? I somehow doubt that Mr. Connelly has ever been in the position to require one himself, so it's not like he can add a valid viewpoint to the discussion. Alas, that complaint seems to be seated in the political and religious viewpoint that has respect for embryonic life but none for humans that can actually walk and talk.
Health care is currently regulated by insurance bureaucrats, most of whom are not health care professionals but paper-pushing clerks who are trying to maximise their profits. Comparing this to the proposed system wherein government bureaucrats would take their place, it amounts to a draw at worst. It's also possible that the government version, not driven by profits, might be just a bit less obnoxious to deal with and result in fewer medical expenses for the patient.
The author asserts that the balance of power between the branches of government will be compromised by a new health care system. He fails to supply anything resembling evidence for this assertion, so I can dismiss it with a similar lack of evidence.
For an instructor of constitutional law, this man's grasp of the constitution seems rather poor (so does his logic for a former attorney, for that matter). I'd speculate that he chased ambulances for a living, but ad homenem aside, we can simply examine his arguments as they stand.
3rd and 4th Amendments> The author maintains that the government having access to your healthcare records, in an effort to maintain that care, amounts to unreasonable search and seizure. Search and seizure of what, exactly? This bases itself on the assumption that there is something sinister involved here, rather than the exact same forces in play that your current health insurance apply. If we really want to get snarky, we can always consider that the Patriot Act did the same thing for any form of electronic communication you might have used while it applied. I'm siginicantly less concerned about the Obama administration having access to my medical records than I am (or was) about Bush and his theocrats having access to anything someone who might not agree with them said on the phone or in an email.
5th Amendment> The argument amounts to stating that paying taxes is tantamount to seizure or property without due process. While that may be a typical Libertarian view, it hasn't been applied to the rest of our tax system, and it's a function of a governed capitalist society that the government has to have money to operate. Somehow I don't see the author of that email donating to them.
The responses to the 9th and 10th Amendments are rather telling, as is the "I defy anyone to show me where it says in the Constitution that the government can regulate health care". Well, Mr. Connelly, since the medical profession in 1789 was also the same profession that was quite capable of giving you a nice shave and a haircut, whilst chopping off a limb or bleeding you because of poor "humours" in the blood, I imagine the founders didn't even consider giving that power explicitly to anyone; Nor did they implicitly give the federal government the power to regulate any other industry, say drug and food safety or worker's rights. As an instructor of Constitutional law, you must surely understand these things we call "implied powers"? We've been using them for about two centuries now.
It's entirely possible that the good lawyer is simply a genuine State's Rights man, of the sort that thinks they should still own slaves and lost a certain war over state's rights about 150 years ago. If so, he should consider encouraging his god-bot infested hellhole of a state to secede again. We wouldn't miss them, and I certainly wouldn't miss the bullshit arguments that he thinks he's provided.

Perhaps the map isn't so far off, but at least that little nation within a nation has shrunk since the map was designed.

Addendum In the interest of fairness, whomever originated the email left off the contact info, not the author. Michael Connelly can be contacted at mrobertc@hotmail.com , and his blog can be found here.

Review of The New Atheism, Victor Stenger

The New Atheism fills a needed gap in the literature begun by Sam Harris in End of Faith, in that it actually addresses all the fleas, and attempts at legitimate rebuttal, that have surfaced in response to the books by Dawkins et. al.. Stenger begins with a solid summary of the works of the "Four Horseman", as well as those by himself and Dan Barker, that also incorporates census data on just how many nonbelievers exist worldwide. This portion of the book, and those dealing with suffering and morality, aren't novel, although they serve to round out the scope of the material.
The key portions of Stenger's book are the rebuttals of Haught, D'Souza, and the ilk who have made legitimate attempts to address the arguments of the New Atheists (at least tried to blow enough smoke in front of them so as to create doubt in those arguments). As I had no interest in purchasing or reading the drivel perpetuated by religious apologists, it is useful to see from whence their arguments might come, as well as to have those arguments examined in clear language. Stenger is concise to the point of almost being too brief in some parts, but manages to address a number of apologetic claims. One can almost imagine a Gish gallop of religious argument that demands rebuttal as the author replies to them. Perhaps more importantly, and more interestingly, Stenger addresses the fine-tuning arguments from physics that previous atheist authors have not touched, ably eliminating that from the viable apologetic arsenal. For clarity's sake, Stenger's refutation amounts to pointing out the the apologists' argument fails to take into account that varying one physical constant actually varies the others and leads to conditions that are still suitable for the organisation of matter and life in some form, although not necessarily life as we know it. The assertion of the theists is thus reduced to special pleading based on the anthropic principle. Furthermore, Stenger poses the multiverse theory, among others, as a manner to resolve the problem of fine tuning. He also points out that the idea of a pre-Big Bang singularity, the point where theists like to insert a deity as a first cause, has been dis-proven in physics since Hawking's Brief History of Time in 1988. William Craig Lane and Dinesh D'Souza still cling to this argument, as do many of their supporters, so Stenger's submission of quantum tunneling from yet another universe as the cause of this universe, supported by publications of both his own and Hawking's, serves as an important nail in that coffin. By simply citing a zero energy beginning to the universe, which is empirically supported, much of the fine tuning argument evaporates of its own accord.
Stenger also devotes a chapter to the mind, as he believes that may be the last real battleground where theists seek to insert god. While scientific notions of mind still have explanatory work to do, Stenger asserts that, as with the evidence of an interventionist deity, the presence of a dualistic mind, that is a mind that arises separately from the matter of the brain, absence of evidence is indeed evidence of absence. The latter phrase is useful in maintaining an agnostic stance toward natural phenomena, however the author makes the valid point that the absence of evidence that should be there if a hypothesis were true disconfirms that hypothesis. This holds true both for a deity that intervenes in the universe and the existence of a (insert religious term for soul here).
The remainder of Stenger's book is devoted to explaining the nature of science, debunking Mormonism and explaining the history of religious phenomena, placing Christianity and Jesus in the proper historical context of an axial age (wherein numerous cultures at the same stage of civilisation had thinkers who professed moral codes), and, surprisingly, agreeing with Sam Harris that Eastern philosophy, once stripped of supernatural pretence, serves as a viable source of morality. In particular, the author seems to admire the eightfold path of Buddhism as a moral code, although he also supports the aspects of Hinduism and Taoism that demand a reduction of ego as a means of living a morally fulfilled life.
While not entirely novel, Stenger's work is concise and well-written, with enough newly presented notions to be worthy of a read. Thanks for the early birthday gift, Mom.

Well, Last Time it Was Sarcastic

... but apparently I am a bit too harsh. A professor in the PhD programme chose tonight to discuss what she terms "professional discourse". I'll boil down her points as I understood them, and then I'll give my take on them.
1. It's not OK to directly confront wrong notions, ideas, and statements. Instead, you need to phrase a rhetorical question or frame the response in such a way that you sound as if you're only giving your view on the subject.
2. Asking for evidence to support an assertion is unreasonable because "we don't have the books in front of us."
3. You need to refrain from using big words, or if you do you should explain what they mean. Using big words make you sound like a know-it-all.
4. Don't dominate the discussion, but don't sit there silent either. By dominating the discussion you're silencing someone else who might want to talk, and sitting silently isn't contributing.

To be fair, I see nothing terribly wrong with #4 provided that other people do actually want to talk. The other three are a bit of an annoyance, and rely upon some poor reasoning.
It's perfectly acceptable to confront some one's wrong ideas with empirically supported ideas of your own. This is called debate, and in the absence of being directly handed information, it's how we might actually learn something from a course web discussion. I agree that it's a logical fallacy, and counterproductive, to attack the person themselves. However, since when does professional discourse have to include deference to absolute horseshit? (oops, I just broke #3, again). Calling the idea horseshit is a bit rude, I'll admit, but demonstrating that it's not correct is another story. We have a style over substance fallacy working here, and apparently it's the dominant culture in the course.
Evidence is how we, as rational human beings, actually support what we're saying and manage to establish some measure of veracity for our assertions. Operating under the assumption that I can just assert something and that should be good enough leads to the submission of personal experience and anecdote as proof of (insert concept here), and just doesn't work. These people are PhD students in Science Education, surely they grasp the idea of evidence? All that aside, how frackin' difficult is it to Google something?
The last sentence applies heavily to #3 as well. You don't know a word I used? Really? All right, I can accept that, now open another browser window and use OED to figure out what it means. Still don't get the concept? Wikipedia is full of entries on just about everything; Not necessarily ones that contain loads of perfectly verified information, but I'm not discussing anything particularly controversial here. Alternately, you might try something like searching the name of the person I just cited, and it's just possible that the very source I used will pop up, or something that at least summarises the ideas espoused in that source.
/rant. Perhaps I should have stuck to the actual sciences, or looked into Philosophy despite my scant background in it if I wanted to be able to have real discussions with people in my programme. Or perhaps these people need to grow a thicker skin, take Sagan's advice and not get so attached to their hypotheses, learn to look things up they don't understand, and possibly provide something to back their assertions beyond "Well, in my experience..."