The Stem Cell Debate is Over?

These were the words of Dr. Oz to Michael J Fox on Oprah earlier this year. Sadly, though the science is settled, the debate rages on. Hopefully that can be changed.

I recently came across this article, which claims that Chinese scientists have created stem cells that are identical to embryonic stem cells. Here's the equivalent article form the Washington Post. So, what did they do, and what does it mean? This isn't supposed to be a comprehensive explanation of the topic, but I hope it will help you to understand the issues. For a more in depth discussion of the science involved you can visit the National Institute of Health. Of course, their information ignores some issues and is a bit out of date on some points, but you get the idea.

What is a Stem Cell?

You are composed of cells, trillions of them. Those cells are all 100% genetically identical, and uniquely you. However, most of your cells have special duties. Cells specialize to perform those duties by differentiating. That means that although they have the same DNA they express it differently. It like everybody having the same song book but reading different musical parts to sing in harmony. So instead of having all identical cells, you have a brain made of brain cells, a heart made of heart cells, skin made of skin cells and so on. If your liver fails, you can't take a kidney and move it to the right place and have it turn into a new liver. Stem cells are cells that aren't differentiated, so they can become other cells.

The hope of stem cell research is that we can learn to grow these cells and teach them to become other cells at will. So, when you have tissue damaged by disease or accident, you can regrow that tissue and replace the damaged part. By regrowing pancreatic cells we could potentially cure diabetes. By regrowing nerve cells we could potentially cure paraplegics, or parkinson's disease patients.

Why are there different kinds of Stem Cells?

Most Americans think (and have been encouraged to think) that stem cells are stem cells. It is unfortunate that the media often doesn't even report what type of stem cells they are talking about, because there are three different kinds, and there are very important differences between them. Let's talk about the different kinds.

At one time you were composed of just one cell, and all of the cells you have now came from that one cell that was you. So, at some point you had cells that could grow into any part of you. These cells are called "stem" cells, because all of the different kinds of cells stem from them. These cells are called embyronic stems cells because they are present in embryos.

Even today, if you get a cut in your skin you can grow new skin over the cut (as long as it's not too big). If you have a heart attack your heart can regenerate new muscle. The cells that can regenerate are also stem cells, but for some reason they can only grow into certain types of tissue. For instance, stem cells from your heart can grow heart tissue but can't grow brain tissue. These cells are called adult stem cells, because they are present in adults.

As I've mentioned, all of the cells in your body have the same DNA. That is to say, they all have the complete song book. So why can't we get the cell to look at the whole "book"; to "undifferentiate", or go back to the state it was in before it became a heart cell or a skin cell? It turns out we can. Scientists have learned to take skin cells and make them revert into stem cells. Cells produced this way are called induced pluripotent stem cells or iPS cells.

There are other types of stem cells, such as fetal and amniotic stem cells, but these are the "big three" that make the news all the time.

What's the difference?

There are drawbacks to each of these types of stem cells. The biggest drawback to embryonic stem cells is not a scientific one, but an ethical one. To extract these cells, an embryo, which is a whole living human being, must be killed. This makes them sort of like, well, Dracula, where the living are sacrificed and their "life essence" extracted to provide the vampire with life. Some scientist, politicians, actors, etc. would have you believe that an embryo is not a living human being, yet it is clearly human, or we could not use the cells, and clearly living, as we are extracting living tissue from it. In fact, just read an embryology textbook and you'll see that they are wrong.

Other scientists et. al. would argue that we'd only kill embryos that nobody wants anyway. That argument doesn't hold water ethically, as it's the same one used to justify the genocide of Jews in Nazi Germany. There is no ethical way known to obtain embryonic stem cells, and scientist, politicians - well, you know how - who say they will use them "ethically" are flat out liars, or completely ignorant of the facts.

OK, that's one drawback, but there are also scientific problems with them. The major scientific problem is related to the ethical problem; they are not your cells. If you attempt to cure diabetes by growing pancreatic cells, you are not growing your own body's pancreas, you are growing someone else's, and so you have all the problems of tissue rejection that people who receive transplants have. Then there is the fact that they don't behave like your own cells, and often go haywire in the environment of your body, turning cancerous.

The state of the art in embryonic stem cells is exemplified by the articles I quoted in an earlier post on stem cells. We see doctors struggling to find a way to keep the stem cells from forming dangerous tumors.

OK, what about adult stem cells? We can take adult stem cells from your body, grow them until we have as many as we need, and insert them back into the body, where they will happily grow into healthy tissue. There is no issue with rejection or cancer, because it is your own tissue. In fact this has been done successfully for many disease over the past years. The drawback is that adult stem cells can only become certain types of tissue, not any type. Therefore you need to take stem cells from the organ that needs to be repaired. Thus, to repair heart tissue, part of your heart needs to be surgically extracted. Also, it is not known how to extract stem cells for some types of tissue. So, while there have been many success stories (in fact, all of the successful "stem cell cures" discovered so far use adult stem cells), there's still a lot of work to be done.

Finally we come to iPS stem cells. These cells are the best of both worlds. Like adult stem cells, they are your own tissue. Like adult stem cells they are ethically "good". Like embryonic stem cells they seem to be able to become more than one type of tissue. So, what's the down side? The key word is seem. Nobody was sure if they coudl actually become any cell, or if embryonic stem cells still had an "edge" in that department.

What does the article really say?

The article I mentioned at the beginning of this post describes experiments done by researchers in China. They took iPS cells from a mouse and grew another complete mouse from those cells! If you can grow a complete organism from a stem cell, then clearly those stem cells are the exact equivalent of embryonic stem cells, and they can become any kind of tissue. This is definite proof, since if the cells couldn't become heart tissue, for example, the resulting mouse wold have no heart and would not live.

Now this does not mean there are no problems with iPS stem cells. We are still learning how to make them and how to use them, but it does mean that there is now no possible reason to use embryonic stem cells for research, as they can be replaced cell for cell by an iPS stem cell that doesn't have the ethical or rejection issues.

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Aborting Health Care

I know I am preaching to the choir, since all 3 of my readers probably know this better than me, but I'd still like to say my piece about why abortion should not be in the health care bill, and specifically should be excluded from it. So hear are my 6 reasons to reject the health care bill as it is written, no matter what your views.

1. Abortion kills a human being. 'Nuff said. But if you don't believe that consider

2. More Americans are pro-life than pro-choice. So, in addition to the above, by passing it our representatives are not representing most Americans, but going counter to the "majority rule" that has been used to justify abortion in the past.

3. It violates Americans' right to conscience. If passed, all American individuals and institutions, including the Catholic church, will be directly funding Planned Parenthood's abortion industry.

4. Even if you are pro-choice, the fact that it's a choice means it is elective surgery. If you think every women has the right to choose an abortion consider that every woman has the right to choose a boob-job, but should we all be forced to pay for it?

5. Even if you are pro-choice and believe that no woman should pressured one way or the other in her choice, consider that by funding abortions we are pressuring women to have them, since the cost after health insurance is higher for keeping the baby. Why not demand funding for pregnancy services and obstetrics to make thing on an even footing economically, and truly trust women to make the choice?

6. Let's say you don't care about abortion, your big issue is the economy. Do you think at this time, when we are trillions in debt, we should be dumping another ton of money, this time to "bail out" an industry that's wildly profitable? Planned Parenthood has (IIRC) $300 million in cash and over $1 billion in assets and we're going to give then an estimated $700 million our of our pockets?

Stop the abortion mandate now!

P.S. As Lavona wrote in her comments, there are many, many more reasons, some of which I was aware of, some not (like hers). you can find more here and here and dozens of other places. Perhaps the bill should be changed to "Eugenics 101".

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Junk? Science?

I recently stumbled upon a "60 Minutes" (for those abroad "60 Minutes" is an hour long weekly news show) video segment from April 22, 2009 (my anniversary! Yay!) about Cold Fusion. "Isn't that just junk science?" you might ask. Well, check out the video and come on back for the rest of this post.

I remember the day 20 years ago sitting in my Bell Labs' office, pondering with my office mate whether or not the discovery would be confirmed. "I'd bet against it" he stated, matter of fact-ly. That way if it's fake at least I win the bet, and if I lose the bet at least we'll have cheap energy. I wasn't such a pragmatist. I really wanted it to work. My friend and I actually spec'd out palladium, so if the experiment were confirmed we could grab some before the price went through the roof and start experimenting with our own cells.

Alas, it was not to be. When the news came that results could not be duplicated, I was crushed. But some people didn't give up hope, and it seems for 20 years they've been trying to duplicate the experiments of Pons and Fleischman, with varying decrees of success. Now, according to 60 minutes, there are a number of experimenters who have results that are indisputable. Of course, most scientists still dispute it, and I would hardly consider 60 Minutes to be my weather vane for science. Still, I hope the effect turns out to be something real, although I'm not pricing palladium this time.

If there's any moral to this story it's this. We are taught in science class, and indeed even in history class that scientific discoveries are absolute and empirical, and that they are based purely on observation, hypothesis, prediction and test, using reason and logic only. The truth of science is it is filled with as much faith, doubt, and uncertainty as the religion some scientists spurn.

So, don't hold your breath, but you might want to look into deuterium futures. What do you think?

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Sell the Vatican!

The other day I was speaking with an "ex-Catholic" friend about faith. There were a number of things we discussed, which I will blog about as time goes by, but one thing was his statement that he can't believe in Catholicism because the Pope doesn't. According to him (and others), if the Pope really believed in Catholicism he would sell all the billions of dollars of art work, all the buildings and land, etc. and give all the money to the poor and ed world hunger once and for all.

There are two aspects of this logic that are mistaken. First off, the notion that "I would believe in 'X' if you did 'Y'" when you know darn well the person isn't going to do "y" is simply making an excuse. If you believe you believe. If you don't you don't. If someone else's actions affect your entire world view, you have a seriously fragile world view, and it will just as easily change next week when someone else does something else. Either an argument is logical or it isn't. The actions of the person who tells you about it doesn't make it any more or less compelling. So right away there is a barrier of insincerity in the question.

Secondly, there are number of reasons for the Pope not selling all the art work and giving the money away and ending world hunger. Before going over them, let's make an analogy. If he cares about poor people, why doesn't the president of the United Stated sell all the monuments and art work and stuff in the Smithsonian, and all the buildings in Washington and give the money to the poor and end hunger and provide health care, etc. for all Americans. Same issues, pretty much.

First off, those things are not the president's (Pope's) to do with as he pleases. They belong to the country (world) and many of them serve good uses, like the stuff the in the Smithsonian (name your favorite place here) that is used for teaching.

Secondly, how effectively could the US (Vatican) conduct its business with no buildings, no staff, no way to communicate or educate? A certain amount of money, and yes, even grandeur is needed to be a "player" in this world.

Lastly, and sadly, all the money in the world would not end world hunger. Throwing money at a problem doesn't make it go away (and often exacerbates it). Let's say you did sell everything off and wanted to use the money to feed the hungry. You'd be getting that money from the very rich, and then turning around and giving it back to buy food. the glut of art work on the market place would make it worthless, and the demand for food would drive food prices up so that you'd wind up doing nothing except lining the pockets of speculators. In a day, or a month, or a year, the food would be gone, the rich would still be rich, and the hungry would be hungry again.

Ultimately the problem of the poor and hungry is caused by the attitudes and actions of billions of people, and cannot be solved by a single act by a single individual, or even a single country. The solution is an economy based not on greed or personal gain, but on justice and charity.

Which brings us to Benedict XVI's recent encyclical, "Caritas in Veritae", or "Charity in Truth." Of course I've only read the first couple of pages (it is quite long), but I have read the blogs and heard others analysis who have read it. No, I'm not being hypocritical, I have started reading it and have preordered the book. I just haven't had time yet to spend reading it online, the only form in which I have access to it right now (and I hate reading things online - as you know I prefer books).

In Caritas in Veritae Pope Benedict XVI discusses how in order to have an economy that is just and vital it must be grounded in respect for human beings. It doesn't describe economic practice, more economic philosophy.

For years I've heard people complaining that the Pope can't tell them anything about sex because he is a virgin. The same people complain that the Pope is one of the richest men in the world. So now that he's talking about money, do you think they'll listen?

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The Catholic Laboratory

The other day I was listening to the SaintCast and caught a blurb about the Catholic Laboratory. This is a web site for a podcast about Catholics and science, and science and Catholics. If you recall, my primary reason for starting this blog was my outrage over Stephen Hawking's false and irrational bashing of the Catholic church. So it was with great interest that I listened to the podcast.

As of now I have listened to the first two episodes and I love it! The podcaster, Ian Maxfield, is intelligent, well spoken and has clearly done his research. I encourage all you readers (yes, both of you) to try it out.

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e-book bash wrap up.

OK, I promised to blog more on e-books, and never did. If you remember the list I did not address.

1. E-book readers suck.
2. E-book readers are hard to use.
3. Professors wanted to be "on the bandwagon".
4. Batteries die.

Quite frankly I'm not sure how much addressing this needs. We've been promised fuel cells and all sorts of batteries that will run for many many hours and can be recharged instantly. The technology isn't there. The long last batteries are proprietary, and batteries I can change quickly and find everywhere don't last.

I have used a Kindle, and although I think it is probably the best e-book reader out there, the speed with which I can turn pages and find an arbitrary spot in a book is pitiful. Not to mention the need to use the tiny keyboard.

Paper is cheap, easy to manipulate, and a pencil is a great annotator. e-books are a solution looking for a problem they can solve better than existing solutions. So for all I would like one, I don't want to give up the convenience of books.

And with that I'm going to go on to other stuff...

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Searching Plurks

How often do you find code in a blog post? I became a plurk fan a while back, but the one feature I missed (and apparently couldn't live without) was a way to "grep" my time line. For non-UNIX geeks, "grep" is a command on UNIX for finding patterns in files. It stands for:

g/re/p

which in the original UNIX editor, "ed" meant globally search for a regular expression and print lines that match.

Here's a sample of how it works:

$ perl plurkgrep.pl young
fetching http://www.plurk.com/m
fetching http://www.plurk.com/m/p/178i6r
fetching http://www.plurk.com/m/p/178g4g
found young in
JeffYoung says On my way to pick up window unit from friend. A/C people won't be able to come until tomorrow at the earliest.
on 2009-07-07 at 00:34

Responses:
kxxn is glad you have that option!
JeffYoung says Me too!

http://www.plurk.com/m/p/178g4g

So, how can I get this goodness? First off, you have to be familiar with a command line.

Save the code below in a file, "plurkgrep.pl" or some such. On a UNIX or Mac you will have to be geeky enough to make it executable and put a header line on it with the locaiton of your Perl binary, or call it as "perl plurkgrep.pl". You may also need to install "Term::ReadKey" from CPAN.

The first time you run it you will have to use the "-u user" option, and it will prompt you for a password. It will store the cookie from plurk.com in a file, plurk.cookie, so you won't have to login every time.

If there's enough interest I could make this into a web page, but it would require users to enter their plurk password and trust me not to misuse it. Let me know what you think!

use LWP;
use Term::ReadKey;
use HTTP::Cookies;

my $sleep = 0;
my $quiet = 0;
my $word = 0;
my $user = '';
my $now = time;
my $then = $now - 14 * 24 * 3600;

my $cookie_jar = HTTP::Cookies->new(file => "$ENV{'HOME'}/plurk.cookies", autosave => 1);
my $browser = LWP::UserAgent->new;
$browser->cookie_jar($cookie_jar);
$browser->agent('Gecko/2009060214 Firefox/3.0.11'); # Pretend to be firefox

# Parse args
while (scalar(@ARGV) > 1) {
    if ($ARGV[0] eq '-u') {
        shift;
        $user = shift;
    }
    elsif ($ARGV[0] eq '-d') {
        shift;
        my $days = shift;
        $then = $now - 24 * 3600 * $days;
    }
    elsif ($ARGV[0] eq '-w') {
        shift;
        $word = 1;
    }
    elsif ($ARGV[0] eq '-q') {
        shift;
        $quiet = 1;
    }
    elsif ($ARGV[0] eq '-h') {
        usage();
    }
}
usage() if (!scalar(@ARGV));

my $term = join(' ', @ARGV);
$term = '\b' . $term . '\b' if ($word);
my $host = 'http://www.plurk.com';
my $url = "$host/m";
my $login_url = "$host/m/login";

$html = fetch($url);
while ($html =~ m!<form action="/m/login" method="post">!) {
    # We need to login
    # read password
    print('Password: ');
    ReadMode('noecho');
    $password = ReadLine(0);
    ReadMode('restore');
    chomp($password);
    my $req = HTTP::Request->new(POST => $login_url);
    $req->content_type('application/x-www-form-urlencoded');
    $req->content('username=' . $user . '&password=' . $password);
    my $res = $browser->request($req);

    # Check the outcome of the response
    if (!$res->is_success) {
        die("POST $login_url failed with " . $res->status_line . "\n");
    }
    $html = $res->content;
}

# We now have first (current) page of plurks
my $next_url = '';
my $time = $now;
while ($time >= $then) {
    my @plurk_html = split(/<div class="plurk">/, $html);
    for my $plurk (@plurk_html) {
        if ($plurk =~ m!<span class="meta">.*<a [^>]* href="([^"]*)">\d*\s*responses?</a>!m) {
            doGrep($1);
        }
    }
    # get next page
    if ($html =~ m!<div\s+class="pagination">\s*[^*]*<a\s+href="(\?offset=(\d+)[^"]*)">next!m) {
        $next_url = $1;
        $time = $2;
    }
    else {
        die("Can't find next page\n");
    }
    $html = timeline("?offset=$time");
}

# We now have all the plurks - fetch each one and do the grep
sub doGrep
{
    my $plurk = shift;
    my $html = fetch("$host$plurk");
    $html =~ s!<h3>Respond:</h3>.*!!m;
    $html =~ s!<h3><a href="#top">back to top</a>[\s\S]*!!m;
    $html =~ s!^[\s\S]*<div class="bigplurk">!!m;
    # clean up formatting
    $txt = $html;
    $txt =~ s!\s+<span class="qualifier [^"]*">([^\<]+)</span>\s+! $1 !gm;
    # remove HTML tags
    $txt =~ s/\<[^\<]+\>//g;
    (my $grep = $txt) =~ s/\s+/ /mg;
    if ($grep =~ m/$term/i) {
        print("found $term in\n$txt\n$host$plurk\n");
        exit(0);
    }
}

sub timeline
{
    my $time = shift;
    return fetch("$url$time");
}

sub fetch
{
    my $url = shift;
    warn("fetching $url\n") unless ($quiet);
    sleep $sleep;
    $sleep = 1;
    my $req = HTTP::Request->new(GET => $url);
    my $res = $browser->request($req);
    if (!$res->is_success) {
        die("GET $login_url failed with " . $res->status_line . "\n");
    }
    return $res->content;
}

sub usage
{
    die <<_;
usage: $0 [-u user] [-d days] [-w] term(s)
    -u user supplies the user name (if you have to login)
    -d days tells how many days back to search (default is 14)
    -w searches for a whole word (so a search for "friend" would not
            match "friendly")
    -q search quietly (see below)
    term(s) a word or phrase to match. Keep in mind you have the full
            power of Perl's regular expressions in searching.

$0 will print out the text of each matching plurk (including replies),
and will also print out the URL of the matching plurk. Because plurk.com has
restrictions on how fast pages can be accessed, $0 pulls down 1
plurk/second. Because of this, it can appear to be stuck, so it prints out
each URL it fetches as it works, so you know it's working. If you don't like
that behavior, -q searches quietly, only printing the result.
_
}

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