Cavalcade of Mammals

A child inherits half each parents genes, and for any individual gene a sibling can either inherit the same or the other allele. Averaged out over the genome, siblings have the same allele for about half the genes.

But genes don’t assort independently of each other, genes are found on chromosomes and due to this inheritance of gene variants is lumpy, a parent has a pair of each chromosome and siblings either get the same chromosome or each gets one of the parent’s pair. This happens randomly for each of the twenty-three pairs of human chromosomes. If humans had only two chromosomes then one forth of the time two siblings would inherit the same pair (out of the four) and be genetically identical. Because humans have twenty-three chromosomes this is vanishingly unlikely. But while on average two siblings have the same gene variant half the time, there is actually a distribution centered at 50%, and siblings can inherit more or less than 50% of same alleles. So how likely are siblings to be 30% or 40% related?

Here’s what the distribution looks like. There are a few more wrinkles to consider. First off, the chromosomes recombine before they assort, so each chromosome a child inherits is a combination of the parents chromosomes. It turns out that in humans, recombination happens more than once per chromosome, about thirty-three times (The Human Genome Project
By Necia Grant Cooper, p31). I include this in my model. I don’t consider the chance that a parent will have two copies of the same allele for a gene, or how recombination is more likely at particular places along a chromosome, or that genes are clumped together in certain chromosomal regions. Here’s the distribution I find:

So siblings don't always share half their gene variants, but rather have a modest chance or being a bit more or a bit less related.


I saw the MythBusters segment on making a boat out of frozen water and wood pulp, called Pyrete. It is essentially a composite material. Pyrete worked pretty good, except for it melting quickly. A boat might last in the Arctic winter for a while if the boat was made from pure water as the salt water there is a few degrees below 0°C. Even at best it would melt over the summer.

This material could be useful if the freezing point could be raised. Unfortunately, most things added to water lower the freezing point. NaCl, table salt, is the best known example. There are ways to raise the freezing point of water–certain organic acids, salts, sugar alcohols. But they require large quantities of additives, so they are either expensive or toxic or both. Too bad.

Explained at Panda’s Thumb:

Over at uncommon descent William Dembski is musing over Richard Dawkins Weasel program. Why you may ask? Way back in prehistory (the 1980’s) Dawkins wrote a little BASIC program (in Apple BASIC of all things) to demonstrate the difference between random mutation and random mutation with selection, which many people were having trouble grasping. Now, this wasn’t a simulation of natural selection, and Dawkins was very careful to point this out.

But as a demonstration of selection versus simple random mutation, with the string “methinks it is a weasel” being selected in a matter of minutes, when simple random mutation would take longer than the age of the Universe, it was pretty stunning. As a result, creationists have been having conniption fits over this little program for decades. Such is its power, the Issac Newton of Information Theory, William Dembski, spent a not inconsiderable portion of his time attacking this toy program. In particular, he claimed that after every successful mutation, the successful mutation was locked into place, and couldn’t be reversed. But he was wrong, and it seems he just can’t admit it.

The Weasel program starts with a random string. Then each generation ‘offspring’ strings are generated, each with one letter randomly changed. From among the offspring, the string closest to the target string is chosen each generation. Rather quickly this process of mutation and selection will change any string into the target string. I start with “Creationism is nonsense” and my target is “methinks it is a weasle”, the target Dawkins uses.

Since the creationists are having trouble making such a program, I wondered *just how short* a program could be written to do this. Here’s a first attempt as a eight line Perl one-liner. It can be cut & pasted into a Unix terminal:

perl -e '$|=1;$s="Creationism is nonsense";$e="methinks it is a weasle";$try=11;$let=length($s);@e=split(//,$e);while($s ne $e){$i=-1;while($i++< $try){$new_s[$i]=$s;$chr=int(rand(27))||-64;substr($new_s[$i],int(rand($let)),1,chr(96+$chr));@spl=split(//,$new_s[$i]);$j=0;$new_sc[$i]=0;while($j<@e){$new_sc[$i]++if$e[$j]eq$spl[$j++]}}@sc=sort{$new_sc[$b]<=>$new_sc[$a]}(0..$#new_sc);@new=(shift@sc);while(@sc&&$new_sc[$sc[0]]==$new_sc[$new[0]]){push@new,shift@sc}$s=$new_s[$new[int(rand(@new))]];printf("Generation %5d, %-2dmismatches:  $sr",++$n,$let-$new_sc[$new[0]]);}print"n";'

(When I cut & paste the one liner on my Mac it changes the final single quote to an end quote and the last two pairs of double quotes to funny double quotes, so keep an eye out and change them back if you need to).

And the normal length 35 line program with comments:

#!/usr/bin/perl

$|=1;
$s="Creationism is nonsense";
$e="methinks it is a weasle";
$try=11; #New offspring per generation.

$let=length($s);
@e=split(//,$e);

while($s ne $e) {
  $i=-1;
  #Make $try new strings.
  while($i++< $try){
    $new_s[$i]=$s;

    #Mutate one char of the new string.
    $chr = int(rand(27)) || -64;
    substr($new_s[$i],int(rand($let)),1,chr(96+$chr));

    #Count the characters in the new string that match the target string.
    @spl=split(//,$new_s[$i]);
    $j=0;
    $new_sc[$i]=0;
    while($j<@e){$new_sc[$i]++ if $e[$j] eq $spl[$j++]}
  }

  #Find high scoring offspring strings.
  @sc = sort {$new_sc[$b]<=>$new_sc[$a]}(0..$#new_sc);

  @new=(shift @sc);
  while(@sc && $new_sc[$sc[0]] == $new_sc[$new[0]]){push @new,shift @sc}

  #Set new string to a random offspring strings from among the high scoring offspring.
  $s = $new_s[$new[int(rand(@new))]];

  printf("Generation %5d, %-2dmismatches:  $sr",++$n,$let-$new_sc[$new[0]]);
}
print"n";

There’s discussion on blogs today about an LA Times editorial highlighting the news that an LA fertility clinic is offering selection of a few non-health related traits in embryos.

This technology was first developed for and used to screen out dangerous genetic disease traits. Couples who both carry the allele for a deadly genetic disease have a 1 in 4 chance of having a child with the disease (in some situations the child would have a 1 in 2 chance). IVF combined with embryo testing allows these couples to have a healthy child. A couple has embryos created through IVF and then a cell from the 8-cell stage embryo is removed and tested for a trait. Apparently some fertility clinics now offer gender selection and will offer selection based on “eye color, hair color and complexion”.

This technology has inherent limits–embryos are being selected from a pool of 6-10 that are created by a round of IVF. So only simple, single gene traits can be picked. If you want a boy the pool is cut in half and now the parents are picking from 3-5 embryos. If both parents have the simplest eye color situation and both carry an allele for blue eyes, 1 in 4 embryos will have it. Parents get at most two choices of simple single gene traits and few traits are determined by a single gene.

Very little is known today about normal human genetics, that is what genes to test for, but that will change and is not an inherent limit to this technology. The curious fact that we know almost nothing about the genetics of normal human traits is a story for another day.

In a few years when we have a better understanding of medical genetics parents will be able to pick the embryos with the fewest and least severe set of disease gene alleles (and even then each embryo will have many bad traits). This choice will for almost all parents trump select of any other trait. Who would pick a green-eyed baby with a 90% lifetime risk of heart disease over a one with a 10% heart disease risk and brown eyes? So concern about IVF clinics offering this is wasted breath, it is a passing notion that will last a few years at most.

This technology has no prospect of offering more detailed choices for parents. More choices would require selecting among more embryos (or among more sperm and eggs), and nothing like that is on the horizon, i.e. it won’t happen in the next thirty years.

Pepper spray has been around for years now, but there is not commonly available antidote. And we know how the active ingredient, capsaicin acts to active, or hold open, the ion channels that transduce pain signals. In fact, a quick Google shows that capsaicin binds and activates a receptor called the vanilloid receptor subtype 1 (VR1), a member of a group of related receptors called TRP ion channels that are activated by temperature changes.

Capsaicin chemical structure (from Wikipedia)

So an antidote would be an inhibitor of the VR1 receptor, and such a thing should be easy to find, or create, and in fact another Google shows that several have been created. Capsazepine was the first inhibitor discovered, way back in 1994. Activators and inhibitors of this receptor have many potential uses as analgesics and anti-inflammation compounds so there is a lot of research interest.

Capsaicin inhibitor capsazepine (from Wikipedia)

A spray containing one of these inhibitors should be an effective antidote for pepper spray. But surprisingly no such inhibitor is available! The small quantities of purified inhibitors are available in small quantities for research purposes (i.e. capsazepine, 50mg for $455 but I can’t find anyone who has made an antidote preparation. This should be safe and fairly easy. Safe, because it would be applied mainly externally, and because pepper spray is itself fairly safe–aside from the pain and shock it is used to cause. It doesn’t have other, non-specific side effects. And relatively easy to make because the literature describes the synthesis of inhibitors from capsaicin itself. So the starting product used to make an inhibitor can be capsaicin, and capsaicin is readily available in large quantities!

Update:
Wikipedia: Discovery and development of TRPV1 antagonists

The first paragraph of Charles Darwin’s Origin of the Species:

INTRODUCTION
WHEN on board H.M.S. Beagle, as naturalist, I was much struck with certain facts in the distribution of the inhabitants of South America, and in the geological relations of the present to the past inhabitants of that continent. These facts seemed to me to throw some light on the origin of species?–that mystery of mysteries, as it has been called by one of our greatest philosophers. On my return home, it occurred to me, in 1837, that something might perhaps be made out on this question by patiently accumulating and reflecting on all sorts of facts which could possibly have any bearing on it. After five years’ work I allowed myself to speculate on the subject, and drew up some short notes; these I enlarged in 1844 into a sketch of the conclusions, which then seemed to me probable: from that period to the present day I have steadily pursued the same object. I hope that I may be excused for entering on these personal details, as I give them to show that I have not been
hasty in coming to a decision.

I’ve never read Origin, having thought of it as mainly of historical interest and not relevant today. But it does have a wealth of examples and descriptions of animals and their niches that now seems interesting to me so I’m having a go it. The Voyage of the Beagle should have even more of this sort of thing, but I figure it makes sense to read Origin first.

It’s funny that Darwin starts his book protesting that he is not hasty. He is the least hasty scientist of which I’ve ever read.

I read today that gorillas weren’t known to people in the West until 1847 when Thomas Staughton Savage described the gorilla from skeletons he obtained. And it wasn’t until later, in 1861 that Paul du Chaillu sent back specimens to England, and the general public became aware of them.

I hadn’t realized that gorillas were discovered in the West so recently. So many fundamental, basic things about the world were first understood in the 1800s. Scientifically it was a time of much greater change than any time before or since.

Chimpanzees and orangutans were sent to Europe in the 17th century. It sounds crazy, but the relationship of humans/chimps/gorillas (human-chimp closest, gorillas more distantly related) wasn’t definitively established until molecular biology techniques were applied in the 1970s! I wonder what Africans thought about chimps and gorillas, and their relationship? I think their ranges overlap in West Africa.

In 1997, the Kyoto Protocol agreement to reduce green gases was signed by 30+ nations including (as best I can tell) all the Western countries except the US. So it was clear in 1997 that the world was warming and green house gas emissions needed to be reduced, but *when* exactly did scientists figure this out?

My memory of the issue with a little proding stretches back to the 1992 climate agreement signed by George HW Bush, officially called the U.N. Framework Convention of Climate Change. It called on countries to cut green house gas emissions but didn’t set binding targets. So global warming was understood back in ’92, and must have been known about years earlier for political action to have been taken then. I didn’t know about research earlier than the 1970s modeling research.

A great talk laying out the history of global warming science by historian Naomi Oreskes is on the web:

She lays out a number of landmarks. She gives an interesting talk–I’ve pared it away and just list the landmarks here:

• 1931, E. O. Hulbert, increasing atmospheric CO₂ 2-3X will lead to 4-7°K increase in world temperature.
• 1938, G. S. Calender, increasing CO₂ leading to increased temps, 1880-1930s
• 1957, Suess and Revelle paper pointing out that dumping back into the atmosphere over a few decades CO₂ stored over millions of years in coal and oil could heat up the world. Calls for detailed research into the world CO₂ budget–where will the CO₂ go, and what secondary effects will there be?
• 1964, NAS committee warns of “inadvertent weather modification” caused by CO₂ from burning fossil fuels.
• 1965, Keeling, about 1/2 of CO₂ from burning fossil fuels will end up in the atmosphere.
• 1965, President’s Science Advisory Committee, Board on Environmental Pollution, by 2000 there will 25% more CO₂ in the atmosphere and marked and uncontrollable changes in climate could occur.
• 1979, JASON committee reports that predicted increases in atmospheric CO₂ will increase world temperature 2.4°C or 2.8°C (two different JASON models). Further, the increase will be much greater at the poles, 10-12°C [Now observed].
• 1979, Charney report summarizes climate science “If CO₂ continues to increase, [we] find no reason to doubt that climate changes will result, and no reason to believe that these changes will be negligible.”
• 1988, IPCC created to study climate and suggest solutions.
• 1988, US National Energy Policy Act, “to establish a national energy policy that will quickly reduce the generation of CO₂ and trace gases as quickly as is feasible in order to slow the pace and degree of atmospheric warming…to protect the global environment.”
• 1992, U.N. Framework Convention of Climate Change
• 1997, the Kyoto Protocol

Most recent numbers I find are from 2005 JAMA study in data through 2003. Total biomedical research is $94.3 billion in 2003, with 57% industry funded and 35% US government funded, 5% state and local, and 3% from private foundations.

This is 5.6% of total US health spending.

Press release for the study.

I’m going to make up my own hydroponics solution. Looking around the web it is hard to find a site with a recipe.

Here’s one at U of Wisconsin-Madison:

0.4 NH4H2PO4; 2.4 KNO3; 1.6 Ca(NO3)2; 0.8 MgSO4; 0.1 Fe as Fe-chelate; 0.023 B as B(OH)3 [boric acid]; 0.0045 Mn as MnCl2; 0.0003 Cu as CuCl2; 0.0015 Zn as ZnCl2; 0.0001 Mo as MoO3 or (NH4)6Mo7O24; Cl as chlorides of Mn, Zn, and Cu (all concentrations in units of millimoles/liter).

Good information from UIUC

and USD.