Open Thread: Pumpkin

Pumpkin

This entry was posted on Friday, October 30th, 2009 at 1:20 pm and is filed under Random Stuff. You can follow any responses to this entry through the RSS 2.0 feed. Both comments and pings are currently closed.

90 Responses to “Open Thread: Pumpkin”

Guts Says:
October 30th, 2009 at 1:48 pm
Is that you in that costume Bradford? Looks cold.

Comment by Guts — October 30, 2009 @ 1:48 pm

Bradford Says:
October 30th, 2009 at 1:57 pm
That's no costume Guts. That's really me. I love pumpkin pie.

Comment by Bradford — October 30, 2009 @ 1:57 pm

Bradford Says:
October 30th, 2009 at 2:43 pm
Congressional ethics report leaks, revealing names

Internal investigations into the conduct of over two dozen House members were exposed in an extraordinary, Internet-era breach involving the secretive process by which Congress polices lawmaker ethics.

Revelations of the mostly preliminary inquiries by the House Committee on Standards of Official Conduct — also known as the Ethics committee — and a panel that refers cases to it shook the chamber as lawmakers were immersed in a series of scheduled votes Thursday.

The panel announced that it was investigating two California Democrats — Reps. Maxine Waters and Laura Richardson — even as its embarrassed leaders took pains to explain that several other lawmakers' names should not have been revealed and they may have done nothing wrong.

Embarrassed? Why is that? Ruined images or real ethical concerns. The former is suspected. These are the same people that bring you new legislation, new policies and new mandates about what you can and cannot do. Transparency in government. The politics of hope. Sad stuff.

Comment by Bradford — October 30, 2009 @ 2:43 pm

Bradford Says:
October 31st, 2009 at 1:40 pm
FACT CHECK: Health insurer profits not so fat

In the health care debate, Democrats and their allies have gone after insurance companies as rapacious profiteers making "immoral" and "obscene" returns while "the bodies pile up."

Ledgers tell a different reality. Health insurance profit margins typically run about 6 percent, give or take a point or two. That's anemic compared with other forms of insurance and a broad array of industries, even some beleaguered ones.

Profits barely exceeded 2 percent of revenues in the latest annual measure. This partly explains why the credit ratings of some of the largest insurers were downgraded to negative from stable heading into this year, as investors were warned of a stagnant if not shrinking market for private plans.

It is sometimes difficult to overcome mythology.

Comment by Bradford — October 31, 2009 @ 1:40 pm

Bradford Says:
October 31st, 2009 at 2:00 pm
From one of America's clearest thinkers:
Dismantling America Will the country wake up before it’s too late?

Just one year ago, would you have believed that an unelected government official, not even a cabinet member confirmed by the Senate but simply one of the many “czars” appointed by the president, could arbitrarily cut the pay of executives in private businesses by 50 percent or 90 percent?

Did you think that another “czar” would be talking about restricting talk radio? That there would be plans afloat to subsidize newspapers — that is, to create a situation where some newspapers’ survival would depend on the government’s liking what they publish?

Did you imagine that anyone would even be talking about having a panel of so-called “experts” deciding who could and could not get life-saving medical treatments?

Scary as that is from a medical standpoint, it is also chilling from the standpoint of freedom. If you have a mother who needs a heart operation or a child with some dire medical condition, how free would you feel to speak out against an administration that has the power to make life-and-death decisions about your loved ones?

Comment by Bradford — October 31, 2009 @ 2:00 pm

ID guy Says:
November 1st, 2009 at 10:53 am
And now for the good news!

olegt has said he is going to stay away from Telic Thoughts as long as I am posting here.

IOW he is taking his ball and going home.

Do all evolutionists act and think like Eric Cartman on South Park?

Comment by ID guy — November 1, 2009 @ 10:53 am

Bradford Says:
November 1st, 2009 at 9:32 pm
The truth matters (for some).

Comment by Bradford — November 1, 2009 @ 9:32 pm

JJS P.Eng. Says:
November 2nd, 2009 at 11:53 pm
From "The Real Wedge-Out of the Closet" Thread:

Rosenhouse: We can make atheism and humanism so ubiquitous and commonplace that the younger generation does not find them weird and exotic. If we are successful the evolution issue will take care of itself.

chunkdz: YES…WE…CAN!!!!

Bob The Builder called. He wants his slogan back or else! And you DON'T want to see Bob's bad side!

Comment by JJS P.Eng. — November 2, 2009 @ 11:53 pm

nullasalus Says:
November 2nd, 2009 at 11:58 pm
ID Guy,

Olegt is a reliable guy. If he says he's not going to post here anymore, he absolutely, positively means.. that he'll be posting in a couple months or so.

Anyway, hello to you. Never saw your posts before (to my knowledge), so greetings and suchlike.

Comment by nullasalus — November 2, 2009 @ 11:58 pm

Tom MH Says:
November 4th, 2009 at 1:13 pm
Where'd the polar bear go? I miss the bear.

What to do with the pumpkins after Halloween, assuming you have more pumpkins than bears and pie can consume.

Comment by Tom MH — November 4, 2009 @ 1:13 pm

Bradford Says:
November 4th, 2009 at 1:29 pm
Tom:

Where'd the polar bear go? I miss the bear.

Someone pulled the plug. It was an internet link that somehow disappeared. Maybe the site owner was anti-telician.

Comment by Bradford — November 4, 2009 @ 1:29 pm

Tom MH Says:
November 4th, 2009 at 1:53 pm
Perhaps it was someone who objected to bandwidth stealing? I suppose the appropriate procedure is to copy the image to one's own web host (or a server such as imageshack) and then link to that. That way you pay for the bandwidth, and you keep your bears.

Not that I always follow this procedure (tsk tsk).

Comment by Tom MH — November 4, 2009 @ 1:53 pm

Bradford Says:
November 4th, 2009 at 2:07 pm
Tom, it's a source I have used before with nary a glitch. A huge website. Maybe some publicity would even up the bandwidth thing if that is the problem.

Comment by Bradford — November 4, 2009 @ 2:07 pm

Salvador T. Cordova Says:
November 6th, 2009 at 11:53 am
Dawkins spends too much time fighting Christianity. Since 911, why have the NA's wasted so much energy on the Christians?????

Fort Hood triggerman: Muslim, shrink

A Muslim U.S. Army officer opened fire at Fort Hood in Texas today, killing 12 soldiers and wounding 31, before he was shot by a base police officer.

The gunman, Maj. Nidal Malik Hasan, orginally was reported to have been killed, but the Army said this evening Hasan is in custody, in stable condition.

The Army Times said Hasan, 39, was a psychiatrist recently reassigned from Walter Reed Army Medical Center in Washington, D.C., to work with soldiers at Darnall Army Medical Center at Fort Hood.

A cousin, Nader Hasan, told Fox News Malik Hasan has "always been a Muslim" and was not a convert as had been reported.

Nader Hasan said his cousin, of Middle Eastern descent, was born in the U.S., attended high school in northern Virginia and graduated from Virginia Tech.

Hasan's name was on a list of officers who received promotions in May, published by the Army Times.

Retired Maj. Gen. Robert Scales told Fox News the massacre did not appear to be the act of a mentally ill or extremely stressed person.

"This was a deliberate act of execution," he said.

Comment by Salvador T. Cordova — November 6, 2009 @ 11:53 am

Bradford Says:
November 6th, 2009 at 12:43 pm
Salvador:

Dawkins spends too much time fighting Christianity. Since 911, why have the NA's wasted so much energy on the Christians?????

Imagine if the gunman had been an evangelical Christian. NAs and far leftists would have a field day. Dawkins and other NAs pay lip service to opposing non-Christian religions but it is clear who the number one public enemy is in their eyes.

Comment by Bradford — November 6, 2009 @ 12:43 pm

Bradford Says:
November 6th, 2009 at 12:56 pm
The unemployment rate has surpassed 10 percent for the first time since 1983 — and is likely to go higher.

Nearly 16 million people can't find jobs even though the worst recession since the Great Depression has apparently ended. The Labor Department said today that the economy shed a net total of 190,000 jobs in October, less than the downwardly revised 219,000 lost in September. August job losses were also revised lower, to 154,000 from 201,000.

But the loss of jobs last month exceeded economists' estimates. It's the 22nd straight month the U.S. economy has shed jobs, the longest on records dating back 70 years.

Counting those who have settled for part-time jobs or stopped looking for work, the unemployment rate would be 17.5 percent, the highest on records dating from 1994.

The jobless rate rose from 9.8 percent in September.

here

The condition for an ended recession has been two consecutive quarters of growth as far as I know. We have not had that so is a recession now ended by fiat?

Comment by Bradford — November 6, 2009 @ 12:56 pm

Bradford Says:
November 7th, 2009 at 12:58 pm
A brewing trade war, initiated by the Obama administration, continues to be waged under the press radar. Of course it is hard to detect what you are not looking for. The most recent volley:

http://news.bbc.co.uk/2/hi/asia-pacific/8345881.stm

Smoot Hawley brought a deep recession into on a full fledged depression around 80 years ago. Those who forget history…

http://en.wikipedia.org/wiki/Smoot%E2%80%93Hawley_Tariff_Act

Comment by Bradford — November 7, 2009 @ 12:58 pm

Zachriel Says:
November 7th, 2009 at 1:30 pm
Bradford: The condition for an ended recession has been two consecutive quarters of growth as far as I know.

The orthodox definition is that two quarters of negative growth constitute a recession. Any quarter with positive growth is not considered in recession.

Comment by Zachriel — November 7, 2009 @ 1:30 pm

Bradford Says:
November 7th, 2009 at 1:43 pm
Zachriel: The orthodox definition is that two quarters of negative growth constitute a recession. Any quarter with positive growth is not considered in recession.

Then the most recent quarter witnessed growth, I take it, which would officially end a recession even if the next quarter gives way to an economic contraction?

Comment by Bradford — November 7, 2009 @ 1:43 pm

Zachriel Says:
November 7th, 2009 at 1:48 pm
Bradford: Then the most recent quarter witnessed growth, I take it, which would officially end a recession even if the next quarter gives way to an economic contraction?

According to the orthodox definition. (There is no official or universally agreed upon definition. Some economists consider unemployment a better gauge.) Of course, if you had two negative quarters, one weak positive, then several more negative quarters, it would probably be considered the same economic cycle (with a blip).

Bradford: A brewing trade war, initiated by the Obama administration, continues to be waged under the press radar.

A key difference between now and time of the Hoover Administration is that each side accepts basic principles of free and equitable trade, with these sorts of disputes now handled by the WTO. The question is whether or not China is dumping in violation of agreements. Nations can still miscalculate, but it does provide some moderate check on behavior and a venue to air grievances.

It is interesting you would point this example, as internationals trade agreements are a bugaboo of the American Right.

Comment by Zachriel — November 7, 2009 @ 1:48 pm

Bradford Says:
November 7th, 2009 at 1:59 pm
Zachriel: A key difference between now and time of the Hoover Administration is that each side accepts basic principles of free and equitable trade, with these sorts of disputes now handled by the WTO. The question is whether or not China is dumping in violation of agreements. Nations can still miscalculate, but it does provide some moderate check on behavior and a venue to air grievances.

I've been doing my homework. This latest action is part of a pattern. US imposition of added tariffs. Chinese retaliation. No outside mediation. Weaker industries on both sides of the Pacific are being protected at the expense of more efficient exporters. The loser in this is the consumer.

It is interesting you would point this example, as internationals trade agreements are a bugaboo of the American Right.

Free trade is strongly supported by conservatives. Agreements do not necessarily enhance free trade. Depends on the details.

Comment by Bradford — November 7, 2009 @ 1:59 pm

Zachriel Says:
November 7th, 2009 at 2:04 pm
Bradford: This latest action is part of a pattern. US imposition of added tariffs. Chinese retaliation. No outside mediation.

Huh? You cited this:

Beijing has filed a World Trade Organisation challenge to US anti-dumping duties on certain types of steel pipes, pneumatic off-road tyres and woven sacks… In August, a WTO panel found in favour of the United States, which claimed that Chinese curbs on importing and distributing foreign publications and audiovisual products violated its WTO commitments.

That doesn't resolve all issues, or necessarily prevent a trade war, but it offers at least some mechanism for the resolution of disputes.

Comment by Zachriel — November 7, 2009 @ 2:04 pm

Bradford Says:
November 7th, 2009 at 2:23 pm
That doesn't resolve all issues, or necessarily prevent a trade war, but it offers at least some mechanism for the resolution of disputes.

Before I put a lot of faith in adjudicating bodies let me see some roll backs. So far what we see is a pattern of increasing trade restrictions.

Comment by Bradford — November 7, 2009 @ 2:23 pm

Daniel Smith Says:
November 8th, 2009 at 5:39 pm
Bradford: Free trade is strongly supported by conservatives.

Not all of them. I am an unabashed political conservative and a 30+ year union member. Free trade has led to the undoing of the manufacturing base of this country. Think of all the industries that used to thrive in this country but now are exclusively based outside the US.
Every other country in the world protects its own industries – we don't.

When US companies compete with foreign companies whose labor costs are far lower, they have one of two choices: lower US wages or move manufacturing operations out of the country. Both are happening at record paces.

Comment by Daniel Smith — November 8, 2009 @ 5:39 pm

Bradford Says:
November 8th, 2009 at 6:24 pm
Daniel Smith:

Not all of them. I am an unabashed political conservative and a 30+ year union member. Free trade has led to the undoing of the manufacturing base of this country.

I differ on this Daniel having owned a small business which has business transactions with manufacturers. Small businesses and manufacturers have seen sharp increases in the cost of doing business over the last few decades. Much of it results from governmental policies. Our trading partners are not responsible for our current economic woes.

Think of all the industries that used to thrive in this country but now are exclusively based outside the US.

This is tragic. But the way to combat this is to create business friendly policies in the USA. Ireland has done so with spectacular results. NJ has gone in the opposite direction and seen a departure of its manufacturing base and the consequent economic hardships and unemployment those policies engender.

Every other country in the world protects its own industries – we don't.

The best way to protect industries is to allow and even encourage entrepreneurs to do what they do best- innovate and create new businesses and jobs. The world needs to decrease governmental involvement in business, not increase that tendency. If you want to see what happens to countries in which the public sector predominates, spend some time in South America. Bureaucrats do not generate wealth.

When US companies compete with foreign companies whose labor costs are far lower, they have one of two choices: lower US wages or move manufacturing operations out of the country. Both are happening at record paces.

It is a mistake to think that wages are the sole indicator of manufacturing decline. Increases in productivity can more than compensate for higher wages. The advantages of advanced technology and new innovations can far outweigh low wages in less advanced nations.

Comment by Bradford — November 8, 2009 @ 6:24 pm

Daniel Smith Says:
November 8th, 2009 at 7:28 pm
Bradford,

I completely agree with reducing regulations and red tape when it comes to business. I think the government should be all about promoting and protecting American businesses – large and small.

What troubles me is that American companies cannot compete against Chinese companies who pay pennies to the dollar for labor. Just go to WalMart and try to find something made in the USA! Our policy for the past few decades seems to be "oh well it's a free market, what are you gonna do?".

I read your link about Smoot Hawley. Some interesting tidbits:

At first the tariff seemed to be a success. According to historian Robert Sobel, "Factory payrolls, construction contracts, and industrial production all increased sharply." However, larger economic problems loomed in the guise of weak banks. When the Kredit-Anstalt Bank of Austria failed, the global deficiencies of the Smoot-Hawley Tariff became apparent.

So Smoot Hawley worked – at least until bank failures derailed the economy.

There is not any universal agreement about the effect of the tariff. According to the U.S. Statistical Abstract, the effective tariff rate was 13.5% in 1929 and 19.8% in 1933 with 63% of all imports being duty-free. From 1821 through 1900 the United States averaged 29.7% effective tariff rates and peaked in 1830 at 57.3% with only 8% of all imports being duty-free, dwarfing the Smoot-Hawley rate. In addition, imports during 1929 were only 4.2% of the United States' GNP and exports were only 5.0%. For monetarist authors who consider the Great Depression an effect of the monetary policy of the Federal Reserve, the Smoot-Hawley's effect on the entire U.S. economy may have been small compared to monetary policy. By 1937 the effective tariff rate was reduced to 15.6% when the reaction of 1937–1938 occurred, demonstrating no statistical correlation between this economic downturn and tariff levels.

A) Smoot Hawley was modest compared to previous US tariffs; B) imports/exports were a small fraction of the US economy at the time of Smoot Hawley; and C) there doesn't seem to be any correlation between higher (1830) and lower (1937) tariffs and economic downturns.

However, the American Tariff League Study of 1951 which compared the effective tariff levels of 43 countries found that only seven countries had a lower tariff level than the United States (5.1%). Eleven countries had effective tariff rates higher than the Smoot-Hawley peak of 19.8% including the United Kingdom (25.6%). The 43-country average was 14.4% ± 0.9% higher than the U.S. level of 1929.

This was in 1951 – seven years after Smoot Hawley was lessened by the Bretton Woods Agreement of 1944, and six years after "a great lessening of global tariffs starting in December 1945".

America has a bad habit of shooting itself in the foot. We're the only country in the world that does not take full advantage of its own natural resources and that fails to protect its own businesses. We should stop that!

Comment by Daniel Smith — November 8, 2009 @ 7:28 pm

Salvador T. Cordova Says:
November 9th, 2009 at 2:26 am
Ok,

Here is one of the animations I was talking about. It takes about 2 minutes to load. It is an mpeg file.

http://www.idcsnetwork.com/audio/nachman.mpg

The creatures are represented by ginger bread men. A harmful mutation is represented by a red dot. Explosions of gingerbread men represent elimination by natural selection. The point is that even after selective sweeps, the collective genome remains irreversibly damaged (represented by the persistence of red dots on the surviving non-exploded gingerbread men).

The goal of the animation was to distill the essential points of graduate level population biology in regards to genetic deterioration to something even a high school senior could understand.

The current estimated mean rate of nearly neutral, but harmful mutations is 300 per human per generation. Even with a several standard deviations from the mean were still talking about easily 100 harmful mutations per individuals. The true number could be in the thousands, but I'm picking 100 as a conservative number.

The animation depicts the inability of selection to weed out such mutations even on the generous assumption we are dealing only with 1 mutation!

Population biology will yet be another theoretical challenge to Darwinism, and I believe this will even be more difficult for Darwinists to come to terms with than Irreducible complexity.

There should be interest in this topic are for its obvious medical implications. Thus, research in this are will proceed independent of whether the ID community is involved or not.

Salvador

PS
I intend to put this up on youtube and post more at UD. TT is getting the first exclusive glimpse of this animation and discussion. Thanks to the folks at TT who have always been supportive of my presence here.

Comment by Salvador T. Cordova — November 9, 2009 @ 2:26 am

Mung Says:
November 9th, 2009 at 4:50 am
Hi Salvador,

Based on this model:

1. what is the absolute longest period of time that humans could have persisted on earth?

2. What is the rate of beneficial mutations that would be required to overcome the deleterious mutations?

thanks

Comment by Mung — November 9, 2009 @ 4:50 am

Zachriel Says:
November 9th, 2009 at 8:42 am
Salvador T. Cordova: The goal of the animation was to distill the essential points of graduate level population biology in regards to genetic deterioration to something even a high school senior could understand.

Graduate level population biology doesn't support the claim of continuing genetic deterioration. The effect you describe is very dependent on the exact model and parameters chosen.

Gregor's Bookkeeper

(Later on that page, and on the next page, there are several charts that show the expected sawtooth pattern.)

Comment by Zachriel — November 9, 2009 @ 8:42 am

Salvador T. Cordova Says:
November 9th, 2009 at 10:53 am
I have policy of not visiting the atbc cesspool.

Sexual recombination will not solve the problem.

If both parents (male and female) are introducing numerous new mutations, how could the genome could possibly purge them.

There is the well known U-Paradox. This animation makes visual the obvious. If the rate of harmfuls is high enough, selection in the way Darwin envisioned is guaranteed to fail.

Try creating an animation to show how that Darwinian selection will be able to clean out the genome under such mutation rates and maybe you can make a believable case.

I repeat:

If the rate of harmfuls is high enough, selection in the way Darwin envisioned is guaranteed to fail.

Do you disagree with that statement or do you think Darwinism can cope with any rate of harmful mutation?

Comment by Salvador T. Cordova — November 9, 2009 @ 10:53 am

Salvador T. Cordova Says:
November 9th, 2009 at 11:08 am
Hi Salvador,

Based on this model:

1. what is the absolute longest period of time that humans could have persisted on earth?

Based on Bryan Syke's work (he is a Darwinist at Oxford), he say's we won't last more than about 200,000 years. That number has been echoed elsewhere. If so, then, one has to ask, how come we're even still alive. That question was echoed by Kondrashov (formerly of Cornell).

Why we have not died 100 times over

His solution is to suggest synergistic epistasis, but the problem is that synergistic epistasis, from a cost stand point, kills off the nearly neutrals at expense of not killing off the worse problems. "synergistic epistasis" only shifts the problem. What I illustrate with truncation selection in the animation is that even giving selection 100% efficiency will not cure the underlying problem of the cost of purifying selection. I then make a comical commentary on the net effect of "synergistic epsistasis".

In bacterial populations where the genome is small and there is a high reproduction rate, there is less threat of genetic deteroration…

2. What is the rate of beneficial mutations that would be required to overcome the deleterious mutations?

thanks

Beneficials might help, but this is like adding 1 improvement to a car (say turbocharging) while 10 other problems are not being dealt with (the tires are blowing out and the spark plugs are failing the points wearing down the oil running lowere, etc.

Back mutations (going from bad back to the original good state) are rare enough to not be much of an effect. I.e. nuclear radiation can break the DNA, it's unlikey nuclear radiations will go to the same loci to revert it back to the good state without first breaking lots of other things.

The benefit of the animation is that it helps the mind resist the sort of obfuscations, evasions, faulty rationalizations being floated around to answer the problem of genetic deterioration.

Comment by Salvador T. Cordova — November 9, 2009 @ 11:08 am

Salvador T. Cordova Says:
November 9th, 2009 at 11:24 am
Nobel Prize winner Muller made an estimate of the tolerable mutation rate.

See: Nobel Prize winner Muller unwitting pioneer of genetic entropy

it would in the end be far easier and more sensible to manufacture a complete man de novo, out of appropriately chosen raw materials, than to try to fashion into human form those pitiful relics which remained…

it is evident that the natural rate of mutation of man is so high, and his natural rate of reproduction so low, that not a great deal of margin is left for selection…

it becomes perfectly evident that the present number of children per couple cannot be great enough to allow selection to keep pace with a mutation rate of 0.1..if, to make matters worse, u should be anything like as high as 0.5…, our present reproductive practices would be utterly out of line with human requirements.

Hermann Muller quoted by John Sanford
Appendix 1, Genetic Entropy

The animation only makes visual what has been known for decades. The animation is intended to help burn through the various obfuscations, rationalizations, and distortions being floated around as a "solution" to an obvious problem for Darwinism and human evolution.

The issue of bacterial evolution is separate.

Comment by Salvador T. Cordova — November 9, 2009 @ 11:24 am

Zachriel Says:
November 9th, 2009 at 3:15 pm
Salvador T. Cordova: If both parents (male and female) are introducing numerous new mutations, how could the genome could possibly purge them.

As I said, we can show it is dependent on the various parameters involved, so a qualitative wave of the hands is not sufficient.

Salvador T. Cordova: Try creating an animation to show how that Darwinian selection will be able to clean out the genome under such mutation rates and maybe you can make a believable case.

I provided that to you, but you didn't bother to look. Others will whether you do or not. Here's the simulation.

Gregor's Bookkeeper

The graphs are available at the previous link.

Salvador T. Cordova:

If the rate of harmfuls is high enough, selection in the way Darwin envisioned is guaranteed to fail.

Do you disagree with that statement or do you think Darwinism can cope with any rate of harmful mutation?

The amount and proportion of deleterious mutations determine whether the process is viable. A simple case; a 100% mutation rate where offspring have no resemblance to their parents. But you conflate that with "if both parents (male and female) are introducing numerous new mutations, how could the genome could possibly purge them?" The answer is that *it depends*.

Salvador T. Cordova: Based on Bryan Syke's work (he is a Darwinist at Oxford), he say's we won't last more than about 200,000 years.

How many generations is that in fly-years?

Comment by Zachriel — November 9, 2009 @ 3:15 pm

Salvador T. Cordova Says:
November 9th, 2009 at 4:18 pm
As I said, we can show it is dependent on the various parameters involved, so a qualitative wave of the hands is not sufficient.

Parameters? Like how many harmful mutations per individual?

Ok, given generous but realistic parameters, what harmful mutation rate (nearly neutrals) can humans tolerate? No hand waving. Some hard numbers. Specify the parameters.

I will not visit ATBC, they are an uncivil mean cesspool. You can provide simple answers for the readers here.

What mutation rate per indivicual is tolerable? Pick the selection coeffients most favorable to your argument, but provide some numbers.

If you don't provide numbers, you're in no position to put forward complaints of hand waving.

How many generations is that in fly-years?

FYI: flies aren't homo sapiens. The reproductive excess is different. Get a clue zach.

Comment by Salvador T. Cordova — November 9, 2009 @ 4:18 pm

Mung Says:
November 9th, 2009 at 4:24 pm
How many generations is that in fly-years?

Considering the OP, I think pumpkin-years would be more appropriate.

Comment by Mung — November 9, 2009 @ 4:24 pm

Zachriel Says:
November 9th, 2009 at 5:17 pm
Salvador T. Cordova: Parameters? Like how many harmful mutations per individual?

Effective population, number of offspring, mutation rate, ratio of beneficial-to-deleterious mutations, and variance in each of these.

Salvador T. Cordova: Ok, given generous but realistic parameters, what harmful mutation rate (nearly neutrals) can humans tolerate? No hand waving. Some hard numbers. Specify the parameters.

I am not making the sweeping claim that a genome can't possibly purge numerous new mutations. You are.

Salvador T. Cordova: I will not visit ATBC, they are an uncivil mean cesspool.

Nobody's perfect.

Here's the software. It's open source.

Comment by Zachriel — November 9, 2009 @ 5:17 pm

Zachriel Says:
November 9th, 2009 at 5:20 pm
When populations fall to very low levels, then minor catastrophes can result in extinction. With Gregor's Bookkeeper, if we set the relative variance to a high level (to represent contingent variations), then it can easily result in extinction. A low reproductive rate also makes a species less robust when populations are at a low level or subject to broad environmental fluctuations. Also important in very small populations is the role of recessive genes due to inbreeding. But in nature, we often expect some hybridization with closely related populations.

Some results of Gregor's Bookkeeper. Here are the settings for this trial. Even with the very low favorable-to-deleterious ratio of 0.00001, the result was an increase in fitness as seen here. You can't see it well, but the fitness drops rapidly at the beginning. It's easier to see in log10. This is because the original population has a uniform (isogenic) fitness of 1, and it takes some time for it to stabilize as a population of nearly neutral mutations.

This gives an idea of the distribution of fitnesses within a population. (The red horizontal line is the mean.) It's fairly uniform except at the margins, but a lot happens at the upper margin. Notice how bottlenecks, though risking extinction, increase overall fitness by weeding out the weakest.

Mutational meltdown is only a plausible problem if a population is kept few in number and genetically isolated for a long period of time. Otherwise, bottlenecks can be evolutionary opportunities.

This has the same settings, but a population of 1000 Parents. It exhibits the same initial decline, but then quickly runs off the chart. Notice the first few turns, as the deleterious mutations precipitate down, and the population diversifies. Then we see fitness stabilize. Later, this population will also increase in fitness.

This one shows growth from an intial population of 1, with topP being 1000. A "founder" population.

Comment by Zachriel — November 9, 2009 @ 5:20 pm

Zachriel Says:
November 9th, 2009 at 5:21 pm
Starting with an isogenic population distorts the initial behavior of the system. If you don't wait long enough, you will reach erroneous conclusions. Consider this example, defaults except numP = 1000 and favMuts = 0.0002. After 25 generations. We see our now well-expected decline. Continuing for 100 turns, we see a bit of an improvement, then stagnation. Stagnation is good. Eventually, we'll see significant, favorable mutations. Here after 200 turns. This is the same settings only favMuts = 0.0001 and a thousand turns.

The key is that there has to be a certain amount of diversity in the population to enable the recombinatorial possibilities. If we just consider the fitness from it's minimum, then the closeup of the previous image looks quite different.

Comment by Zachriel — November 9, 2009 @ 5:21 pm

Salvador T. Cordova Says:
November 9th, 2009 at 5:29 pm
Say again zach, what is the harmful mutation rate per human per generation that can be tolerated?

I missed your answer in your obfuscations and misdirections.

For the benefit of the reader, a simple number will do.

Comment by Salvador T. Cordova — November 9, 2009 @ 5:29 pm

Zachriel Says:
November 9th, 2009 at 5:56 pm
Salvador T. Cordova: Say again zach, what is the harmful mutation rate per human per generation that can be tolerated?

I never made a claim in that regard. But *you did* when you suggested that a genome can't possibly purge numerous new mutations.

The model shows that a small population of ten thousand and a favorable-to-deleterious ratio of 1:100000 easily overcomes "genetic entropy." Like all models, it's a simplification. It shouldn't be considered quantitatively predictive.

Comment by Zachriel — November 9, 2009 @ 5:56 pm

Satolep Says:
November 9th, 2009 at 6:35 pm
I will not visit ATBC, they are an uncivil mean cesspool. You can provide simple answers for the readers here.

What about taking your clue from the lotus flower, growing in the mud, but always above it: (I was taught by Guru Maharaj Ji)

The Son of man came eating and drinking, and they say, Behold a man gluttonous, and a winebibber, a friend of publicans and sinners. But wisdom is justified of her children.

Sophia always was, and (almost) is my one and only love.

Comment by Satolep — November 9, 2009 @ 6:35 pm

Daniel Smith Says:
November 9th, 2009 at 8:48 pm
Zachriel and Salvador,

In the absence of the selecting drugs, chromosomal mutations for resistance to antibiotics and other chemotheraputic agents commonly engender a cost in the fitness of microorganisms. Recent in vivo and in vitro experimental studies of the adaptation to these "costs of resistance" in Escherichia coli, HIV, and Salmonella typhimurium found that evolution in the absence of these drugs commonly results in the ascent of mutations that ameliorate these costs, rather than higher-fitness, drug-sensitive revertants.

here

So even though reversion to the wild type represents a fitter state – organisms are much more likely to live with the degraded genome and rely upon compensatory mutations to alleviate some of that lack of fitness.

Here we have empirical evidence that even a beneficial mutation "commonly" results in a loss of overall fitness, thus requiring new, compensatory beneficial mutations. How many "beneficial" mutations are required to get back to the organisms original state of fitness?

It appears from this that evolution always take the path of least resistance. In something as simple as bacterium this may work out, but in something as complex as humans, the odds are probably much worse.

Comment by Daniel Smith — November 9, 2009 @ 8:48 pm

Salvador T. Cordova Says:
November 9th, 2009 at 8:56 pm
I never made a claim in that regard. But *you did* when you suggested that a genome can't possibly purge numerous new mutations.

If you believe Darwinism for human evolution is true, then it stands to reason you believe the harmful mutation rate is tolerable. Thus surely you have:

1. an estimate of what harmful mutation rate would be tolerable
2. an estimate of what the mutation rate actually is

Without that, you're just accepting it on faith, which is ok, but perhaps you should admit you accept Darwinism in the absence of actual theory and data.

What do the Atbc boys have to say for what harmful mutation rate is tolerable for humans. Hermann Muller (of Muller's ratchet fame) presented a guess of 0.1

I said 100 would surely be too much. Do you have a problem with that?

Any takers for numbers. 1, 2, 3, 4……???

Muller suggested 0.1. What say you and the ATBC friends?

C'mon, I'm only asking for a single measily guess of a number.

Comment by Salvador T. Cordova — November 9, 2009 @ 8:56 pm

Salvador T. Cordova Says:
November 9th, 2009 at 9:05 pm
The model shows that a small population of ten thousand and a favorable-to-deleterious ratio of 1:100000 easily overcomes "genetic entropy." Like all models, it's a simplification. It shouldn't be considered quantitatively predictive.

That doesn't answer the question of how many harmful mutations per human per generation.

A "favorable-to-deleterious ratio" is not an answer to my question, sorry. You answered a different question than the one posed to you.

Let me splain why I think you're response is woefully inadequate. If we have 100 beneficial and 100,000*100 = 10 million bad mutations per person per generation, that obeys the ratio you suggested. Do you think the genome will survive with each person putting in 10 million bad mutations per generation per person? That sounds preposterous. Instead of one red dot in my animation, you'll have 10 million with each round. Does survival and glowing health sound like a believable outcome in such a scenario?

Thanks for at least the effort in putting a response.

Comment by Salvador T. Cordova — November 9, 2009 @ 9:05 pm

Zachriel Says:
November 9th, 2009 at 9:07 pm
Daniel Smith: In something as simple as bacterium this may work out, but in something as complex as humans, the odds are probably much worse.

Think about what you're saying. The bacteria will retain some antibiotic resistance, and make multiple modifications to other systems, a series of complicated, interlocking relationships.

Comment by Zachriel — November 9, 2009 @ 9:07 pm

Zachriel Says:
November 9th, 2009 at 9:16 pm
Salvador T. Cordova: A "favorable-to-deleterious ratio" is not an answer to my question, sorry. You answered a different question than the one posed to you.

I've provided all the parameters for the model. I can't make you look at them.

Salvador T. Cordova: If you believe Darwinism for human evolution is true, then it stands to reason you believe the harmful mutation rate is tolerable. Thus surely you have:

1. an estimate of what harmful mutation rate would be tolerable
2. an estimate of what the mutation rate actually is

Sorry, but that doesn't follow. We can be ignorant of one aspect of a problem, but be aware of another. In this case, I doubt there is an accurate answer to your question. On the other hand, we have strong scientific reason to believe that humans evolved from more primitive organisms.

You suggested that a genome can't possibly purge numerous new mutations. I provided evidence that this is not a significant problem, evidence you have refused to consider. You keep refusing to support your position, so I will take that as a retraction.

Comment by Zachriel — November 9, 2009 @ 9:16 pm

ID guy Says:
November 9th, 2009 at 11:00 pm
Zachriel:
On the other hand, we have strong scientific reason to believe that humans evolved from more primitive organisms.

Which were also human.

There isn't any scientific evidence that supports the claim that humans evolved from primitive non-humans.

Just sayin'

Comment by ID guy — November 9, 2009 @ 11:00 pm

Salvador T. Cordova Says:
November 10th, 2009 at 1:22 am
I've provided all the parameters for the model. I can't make you look at them.

So for the reader's benefit Zach, tell us again how many harmful mutations per generation per human the human race can tolerate?

Muller offered his estimate. What is yours?

A single number would suffice.

Comment by Salvador T. Cordova — November 10, 2009 @ 1:22 am

Zachriel Says:
November 10th, 2009 at 8:55 am
Salvador T. Cordova: So for the reader's benefit Zach, tell us again how many harmful mutations per generation per human the human race can tolerate?

My Goodness, Salvador T. Cordova, I answered your question, several times and several different ways. As I said, I doubt there is an accurate, quantitative answer to your question. But I never claimed to have such an answer. You did.

Your suggestion that a genome can't possibly purge numerous new mutations is unfounded. I provided a suitable, open-source model. I provided results of that model which show that evolution is viable even with large numbers of deleterious mutations. The exact number depends on population, mutation rate, ratio of favorable-to-deleterious mutations, fecundity, minimum viability, and variance in each of these.

Instead of defending your claim, you simply pretend I didn't answer. I not only answered, but I provided reams of data.

- You can lead a person to knowledge, but you can't make them think.

Comment by Zachriel — November 10, 2009 @ 8:55 am

ID guy Says:
November 10th, 2009 at 9:25 am
Zachriel:
You can lead a person to knowledge, but you can't make them think.

That sums up Zachriel very nicely.

Good job!

Comment by ID guy — November 10, 2009 @ 9:25 am

Salvador T. Cordova Says:
November 10th, 2009 at 12:30 pm
Your suggestion that a genome can't possibly purge numerous new mutations is unfounded.

Ok, so how much amounts to numerous? Are you saying the genome can't purge 100,000 new harmful mutation per peson per generation.

If I claimed: "selection can't purge 100,000 new harmful mutation per person per generation" would that claim be unfounded?

You can lead a person to knowledge, but you can't make them think.

It's true I'm a little dense, so can you do some thinking out loud for me and the TT readers?

How many new harmful mutations again can the human race tolerate per generation per human. You said my claim of "numerous" was unfounded. So how many harmfuls per human per generation again is numerous but still tolerable?

10,000,000 (Zach's estimate?)
1,000,000
100,000
10,000
1,000
100 (Salvador's conservative estimate)
10
1
0.1 (Hermann J. Muller, nobel prize winner in medicine for his work on mutation)

Pick a number that's in your ball park definition of numerous.

Comment by Salvador T. Cordova — November 10, 2009 @ 12:30 pm

Salvador T. Cordova Says:
November 10th, 2009 at 12:43 pm
For the reader's benefit, my understanding is that Zach is saying:

1. my quantitative claims are demonstratably false
2. but simultaneously Zach can't give an accurate quantitative answer

So if I said: "100 new harmful mutations per person per generation is too much for selection to purge" Zach claims that number is false even though he himself is unwilling to say what number his model says is tolerable.

Fine, I'll keep upping the number till we reach 1 billion, until he defines what "numerous" means.

The animation suggests that even "1 new harmful per person per generation" is too much. Basic logic would say that is reasonably ball park figure. What does Zach's model say we can tolerate?

Help me zach, I got lost in all the numbers you provided. How much is numerous again? If I claimed "100 new harmful mutations per person per generation is too much for selection to purge", does your model disagree with that? Does your model say somehow on average if 100 new harmfuls per new human are being added, somehow selection over time will cleanse the population. Somehow the accounting wouldn't seem right as illustrated by the animation (and the animation was illustrating a measily 1 new harmful per new human).

Comment by Salvador T. Cordova — November 10, 2009 @ 12:43 pm

Daniel Smith Says:
November 10th, 2009 at 12:50 pm
Zach: Think about what you're saying. The bacteria will retain some antibiotic resistance, and make multiple modifications to other systems, a series of complicated, interlocking relationships.

At the expense of overall fitness.

So is it…
Survival of the fittest?
Or, path of least resistance?

Comment by Daniel Smith — November 10, 2009 @ 12:50 pm

Zachriel Says:
November 10th, 2009 at 1:07 pm
Salvador T. Cordova: 1. my quantitative claims are demonstratably false

You have incorrectly characterized my position—again. Your claim is *unfounded* and contrary to many other lines of evidence. I provided a suitable, open-source model to show why your argument fails—which you have ignored.

Comment by Zachriel — November 10, 2009 @ 1:07 pm

Zachriel Says:
November 10th, 2009 at 1:11 pm
Daniel Smith: At the expense of overall fitness.

Fitness is determined by the environment. So, no. And you still didn't respond to the argument. We end up with a more complicated and more flexible organism.

Comment by Zachriel — November 10, 2009 @ 1:11 pm

ID guy Says:
November 10th, 2009 at 2:14 pm
It would all depend on how "harmful" the mutation(s) is/ are.

It's sort of like getting to the middle of a tootsie-pop.

How good are your teeth and how powerful is your bite?

Then there are epigenetic factors- lose the ability to synthesize vitamin C but eat the foods that provide it.

So like "Name That Tune", we could get a death sentence from a few "key" changes- perhaps even one. Or perhaps the tune just plays on and on.

And sometimes- no matter what variation you have- mother nature slaps you down anyway.

The number for how many harmful mutations can accumulate would depend on what they impact (how vital is it?), how do they impact it and what variation tolerance can be sustained. And if I lose it can I get it from another source.

Comment by ID guy — November 10, 2009 @ 2:14 pm

Salvador T. Cordova Says:
November 10th, 2009 at 4:36 pm
Zach wrote:

You have incorrectly characterized my position—again. Your claim is *unfounded* and contrary to many other lines of evidence. I provided a suitable, open-source model to show why your argument fails—which you have ignored.

Help me out understanding the open source model Zach. How many harmful mutations per new human does your open source model say we can tolerate? I'm not ignoring the model, I'm merely asking that you help me understand what your model says.

How many harmful mutations per new human does your open source model say we can tolerate? Help me out here.

What ball park figure does it give for harmful mutations per new born human?

10,000,000
1,000,000
100,000
10,000
1,000
10010
1
0.1

Comment by Salvador T. Cordova — November 10, 2009 @ 4:36 pm

Salvador T. Cordova Says:
November 10th, 2009 at 4:59 pm

Daniel Smith:

It appears from this that evolution always take the path of least resistance. In something as simple as bacterium this may work out, but in something as complex as humans, the odds are probably much worse.

One solution to the problem of harmful mutations is the on-the-fly redefinition of "harmful". In population biology we call this "re-normalization".

For example human sickle-cell anemia, human cystic fibrosis, human tay-sachs disease, etc., blindness in cavefish, winglessness in beetles, damaged bacterial pumps in antibiotic resistance, damaged cytoskelotons in pesticide resistant insects, etc.

We relabel such harmful mutations to be "beneficial" since they aid in supposed reproductive fitness, but long term they are damaging to the complexity and functioning of the organism.

When a Zeppelin is in trouble and needing to climb it can jettison its functioning equipment in order to lose weight. It is like amputating an organ. In like manner, creating dysfunction can lead to reproductive "fitness". This was especially obvious in Spiegelman's Monster.

That is essentially the solution to some of the population biology problems with harmful mutations. As long as the organism is reproducing more, the problem of harmfuls is supposedly dealt with.

Hence we have notions like Moalem's Survival of the Sickest. It guarantees the notion of "survival of the fittest" will always be true by redefining what it means to be fit. By that standard, even big rocks propagating into numerous pebbles can be considered an example of survival of the fittest.

However solving the problem of harmful mutations via re-definitional gimmickery comes at cost. It decouples any claim that selection will lead to complex function since now selection becomes essentially a random walk where expedience often takes precedence over increase in complexity.

One way to cut through all the nonsense is to see how well selection can purge away any sort of novelties in the genome. This can be measured by tracking the emergence and persistence of single point mutations (single nucleotide polymorphisms) in the human population. The ground work for this is being laid out by the medical community in order to track diseases….

What I expect to see is that selection cannot possibly police all the novelties being introduced into the genome. Independent of the severity of the effects on reproduction or the selection coefficients of these novel mutations, we can make statements empirically on how well selection can police them.

Bottom line: if the number of single nucleotide polymorphisms continues to rise, one has to wonder how much an effect selection has on the genome period!

The animation makes clear that it is not a matter of the kind or intensity of selection being applied, it is a matter that with enough mutation, short of extinction, killing off more organisms won't really stop the deterioration.

It can be argued that selection can't stop the deterioration, and in some cases (like sickle cell anemia and cystic fibrosis), selection actually accelerates the deterioration.

Comment by Salvador T. Cordova — November 10, 2009 @ 4:59 pm

Zachriel Says:
November 10th, 2009 at 5:27 pm
Salvador T. Cordova: How many harmful mutations per new human does your open source model say we can tolerate?

Unlike yourself, I haven't claimed that a simplified, abstract model can provide completely accurate, quantitative results with regards to complex organisms. It does, however, provide sufficient data to show that your original claim is not sufficiently robust to support your overly broad claim.

Salvador T. Cordova: What ball park figure does it give for harmful mutations per new born human?

This doesn't directly answer your question, but assuming you are actually interested, the rate of deleterious mutations in humans has been estimated as about three per individual.

Nachman & Crowell, Estimate of the mutation rate per nucleotide in humans, Genetics 2000.

Comment by Zachriel — November 10, 2009 @ 5:27 pm

Zachriel Says:
November 10th, 2009 at 7:44 pm
Salvador T. Cordova, You might find this paper interesting. The authors investigate how synergistic epistasis and sexual selection affect genetic load.

Whitlock & Bourguet, Factors affecting the genetic load in Drosophila: synergistic epistasis and correlations among fitness components, Evolution 2000.

Comment by Zachriel — November 10, 2009 @ 7:44 pm

ID guy Says:
November 10th, 2009 at 8:26 pm
Yes Zachriel, in a designed world I would expect there to be error-correcting processes.

Comment by ID guy — November 10, 2009 @ 8:26 pm

Salvador T. Cordova Says:
November 11th, 2009 at 1:44 pm
Zachriel:

Unlike yourself, I haven't claimed that a simplified, abstract model can provide completely accurate, quantitative results with regards to complex organisms. It does, however, provide sufficient data to show that your original claim is not sufficiently robust to support your overly broad claim.

What do you mean Zach?

If I claim that 100 new harmful mutations per every human born could not be purged by natural selection (or any selection mechanism for that matter), are you saying I'm wrong?

If you are saying I'm wrong, then you are implying that humans can tolerate a harmful mutation rate of 100 or more new harmful per new born human.

If you're saying my models aren't sufficiently robust, then tell me what the a more robust model might say. If a more robutst model will say my claim is wrong, then fine, that model says the human race can tolerate 100 new harmful mutations per new born human.

So what say you Zach? You said my claim (of 100) is unsupported. Are you also saying my claim is demonstratably wrong? If you say that it is demonstratably wrong, then you are also implying that the figure of 100 is a tolerable amount per human.

So what say you Zach. I claim a harmful mutation rate of 100 per new born human can't be purged by selection (the animation was intended to help visualize the difficulty). Are you saying my claim is wrong, that it has been falsified?

Comment by Salvador T. Cordova — November 11, 2009 @ 1:44 pm

Salvador T. Cordova Says:
November 11th, 2009 at 2:05 pm
For the WEASEL defenders out there, especially those who say WEASEL doesn't partition….

Consider a non-partitioned WEASEL. Assume a beneficial to harmful ratio of 1 to 100,000 (as Zach suggested above), and a mutation rate of 100 per WEASEL phrase (well the WEASEL genome is too small to have a hundred mutations, so even if we mutate every position, we still don't have 100 mutations, but let's grant that since we can't mutate 100, will mutate whatever number is allowable based on the number of positions).

One effectively scrambles the entire phrase every generation. Even in the unlikely event "METHINKS … WEASEL" is hit, in the next few generations, it is gone.

The defenders of a non-partitioned WEASEL have their challenges too.

Perhaps an animation of a non-partitioned WEASEL would be informative under Zach's claim that a beneficial to harmful ratio of 1 to 100,000 is tolerable.

Comment by Salvador T. Cordova — November 11, 2009 @ 2:05 pm

Zachriel Says:
November 11th, 2009 at 5:42 pm
Salvador T. Cordova: If I claim that 100 new harmful mutations per every human born could not be purged by natural selection (or any selection mechanism for that matter), are you saying I'm wrong?

I'm saying your argument, consisting as it is of an animation of gingerbread and a claim to certainty, is unfounded. Your gingerbread model indicates that every child will be a mutant, and as the vast majority of those mutations will be deleterious, your model projects ever-declining fitness. It's a very simple model, but incomplete.

There is a phenomena called genetic load, but there are also a variety of other factors involved that you have repeatedly refused to discuss. Gregor's Bookkeeper is a qualitative model of those factors. We can show that even if every child is a mutant, that for a wide variety of parameters, the population can remain viable.

Salvador T. Cordova: Are you also saying my claim is demonstratably wrong?

No. As I've repeatedly stated, it's unfounded. And as I stated way up above, there is a limit to the maximum mutation rate for sustainable replication.

Salvador T. Cordova: One effectively scrambles the entire phrase every generation.

So far you have effectively set the maximum mutation rate to 100%. Basic mathematical modeling suggests that the error rate can't be more than 5% for simple replicators. Evidence suggests that life tends to operate close to the error threshold of no more than a few phenotypically significant mutations per genome replication (Joyce 2002). This allows maximum evolutionary flexibility with sustainable replication.

Comment by Zachriel — November 11, 2009 @ 5:42 pm

Daniel Smith Says:
November 11th, 2009 at 8:41 pm
Zach: Fitness is determined by the environment. So, no.

Actually yes, they were specifically dealing with drug-resistant bacteria in a drug-free environment. And it was the author's claim that drug resistance "commonly" results in a loss of overall fitness – not mine.

And you still didn't respond to the argument. We end up with a more complicated and more flexible organism.

How is it more complicated?
How does "complicatedness" relate to fitness or to selection?

How exactly do the new mutations increase "flexibility"? Be specific. I can see antibiotic resistance as helpful – when in that environment – but what is lost in the process, and how does that loss affect overall fitness in a sans-drug environment? Also how does it affect overall fitness in the presence of the drug? At the end of the day, are these bacteria more or less fit than the wild type?

Comment by Daniel Smith — November 11, 2009 @ 8:41 pm

Daniel Smith Says:
November 11th, 2009 at 8:44 pm
Salvador: What I expect to see is that selection cannot possibly police all the novelties being introduced into the genome.

This sounds like a prediction that can be empirically verified Sal. I thought IDers didn't do that!

Comment by Daniel Smith — November 11, 2009 @ 8:44 pm

Zachriel Says:
November 11th, 2009 at 9:53 pm
Zachriel: Think about what you're saying. The bacteria will retain some antibiotic resistance, and make multiple modifications to other systems, a series of complicated, interlocking relationships.

Daniel Smith: At the expense of overall fitness.

Zachriel: Fitness is determined by the environment. So, no.

Daniel Smith: Actually yes, they were specifically dealing with drug-resistant bacteria in a drug-free environment. And it was the author's claim that drug resistance "commonly" results in a loss of overall fitness – not mine.

They state the environment at issue. "In the absence of the selecting drugs, chromosomal mutations for resistance to antibiotics and other chemotheraputic agents commonly engender a cost in the fitness of microorganisms." Your original statement was not so qualified.

Zachriel: And you still didn't respond to the argument. We end up with a more complicated and more flexible organism.

Daniel Smith: How is it more complicated?

Because it requires many things rather than one thing.

Daniel Smith: How does "complicatedness" relate to fitness or to selection?

It's just an example of how complex interactions can evolve.

Daniel Smith: How exactly do the new mutations increase "flexibility"? Be specific.

The mutant with compensatory mutations can compete in multiple environments.

Daniel Smith: At the end of the day, are these bacteria more or less fit than the wild type?

It depends on the environment, of course. Over time, compensatory mutations can "restore the efficacy of translation to nearly wild-type levels." It doesn't happen in practice due to the relative brevity of infection followed by the bottleneck during transmission. Nevertheless, pathogens continue to eat people. The authors clearly believe that understanding evolution will help prevent more people being eaten.

Comment by Zachriel — November 11, 2009 @ 9:53 pm

Salvador T. Cordova Says:
November 11th, 2009 at 10:20 pm
Cordova: If I claim that 100 new harmful mutations per every human born could not be purged by natural selection (or any selection mechanism for that matter), are you saying I'm wrong?

Zach:

I'm saying your argument, consisting as it is of an animation of gingerbread and a claim to certainty, is unfounded. Your gingerbread model indicates that every child will be a mutant, and as the vast majority of those mutations will be deleterious, your model projects ever-declining fitness. It's a very simple model, but incomplete.

Say what zach, the estimated rate of harmful mutation per new born is on the order of 300! I greatly understated mainstream estimates in the animation.

your model projects ever-declining fitness.

ever declining functional complexity is a more correct statement.

Cordova: If I claim that 100 new harmful mutations per every human born could not be purged by natural selection (or any selection mechanism for that matter), are you saying I'm wrong?

Let me put it to you more bluntly. Am I wrong to claim: "100 new harmful mutations per every human born could not be purged by natural selection (or any selection mechanism for that matter)".

If you think I'm wrong, say so. If you think I'm right say so. If you're uncertain whether I'm right or wrong say so.

What I sense is that you want to say on one hand, Salvador can't be possibly right, yet on the other hand, you claim we can't have certainty whether my claim is right or wrong.

You seem unwilling to provide simple direct, straight forward answer to what you really think. 3 options about 100 deleterious mutations:

1. you think my claim is right
2. you think my is wrong
3. you don't know or you are undecided

Independent of the gingerbread animation, I don't think the human race can survive 100 deleterious mutatons per new born human. That is the claim that is really in question.

Comment by Salvador T. Cordova — November 11, 2009 @ 10:20 pm

Salvador T. Cordova Says:
November 11th, 2009 at 10:23 pm
This sounds like a prediction that can be empirically verified Sal.

Dang right it can be verified. The medical community is already working on these issues for reasons independent of the ID/Darwin debate.

The tracking of the increase in single-nucleotide-polymorphisms is of keen interest since it is an indicator of various heritable diseases.

Comment by Salvador T. Cordova — November 11, 2009 @ 10:23 pm

Salvador T. Cordova Says:
November 11th, 2009 at 10:25 pm
Rage Genetic Conditions on the Rise

University of Melbourne Professor of Medical Genetics Bob Williamson (Paediatrics, Royal Children's Hospital) has commented on the rise of Australians who are living with rare and often recently identified genetic conditions, in an article in The West Australian.

Professor Williamson explains: 'It isn't so much that the number of people affected are going up it's more that the number of diseases that we recognise is increasing,"

'There are now seven or eight thousand different genetic diseases known to occur, although many of them only affect a handful of children.'

Read more: 'Rare genetic conditions on the rise' The West Australian

Comment by Salvador T. Cordova — November 11, 2009 @ 10:25 pm

Zachriel Says:
November 12th, 2009 at 8:41 am
Salvador T. Cordova: Say what zach, the estimated rate of harmful mutation per new born is on the order of 300!

Most of which have no phenotypic effect.

Salvador T. Cordova: If you think I'm wrong, say so.

Your argument is unfounded. A clear quantitative answer may not be available—as I already stated. Nor would a simplistic model as you propose throw into question the vast amount of evidence supporting Common Descent. It would probably mean your model is flawed somehow. There are better models that compare much more closely to biological reality. I have already mentioned several times the limitations of your model (or illustration), and you have simply refused to discuss it.

Salvador T. Cordova: Independent of the gingerbread animation, I don't think the human race can survive 100 deleterious mutatons per new born human.

Perhaps not. However, that high a rate of deleterious mutations doesn't seem to be the case.

Nachman & Crowell, Estimate of the mutation rate per nucleotide in humans, Genetics 2000. (Nachman is the name of your gingerbread animation.)

Comment by Zachriel — November 12, 2009 @ 8:41 am

ID guy Says:
November 12th, 2009 at 8:47 am
Who cares about accumulating harmful mutations?

What people like Zachriel require are mutations that accumulate in such a way as to produce new molecular machinery, new body parts and new body plans.

To date such evidence has been missing.

Which makes me want to ask just WTF is their "theory" based on?

Comment by ID guy — November 12, 2009 @ 8:47 am

Zachriel Says:
November 12th, 2009 at 8:53 am
Salvador T. Cordova: Rare Genetic Conditions on the Rise

That's funny. The headline directly contradicts the content.

Professor Williamson explains: 'It isn't so much that the number of people affected are going up it's more that the number of diseases that we recognise is increasing,"

Furthermore:

'There are now seven or eight thousand different genetic diseases known to occur, although many of them only affect a handful of children.'

Here's a model that addresses relaxed selection in modern humans.

Eyre-Walker et al., The Distribution of Fitness Effects of New Deleterious Amino Acid Mutations in Humans, Genetics 2006.

We argue that the relaxation of natural selection due to modern medicine and reduced variance in family size is not likely to lead to a rapid decline in genetic quality, but that it will be very difficult to locate most of the genes involved in complex genetic diseases.

Comment by Zachriel — November 12, 2009 @ 8:53 am

ID guy Says:
November 12th, 2009 at 9:19 am
It is also very noticeable that we have a handle of genetic diseases and malfunctions but no one knows if functional and useful new molecular machines can arise via mutations.

And no one knows if body plans can change due to mutations.

Comment by ID guy — November 12, 2009 @ 9:19 am

Salvador T. Cordova Says:
November 12th, 2009 at 10:38 am

you have simply refused to discuss it.

No I have not refused. You have avoided answering the question.

I've asked repeatedly, do those models say we can survive 100 harmful mutations per new born human? Or better yet, do those models predict that selection will cause a net decrease in the harmfuls over time?

Salvador: Independent of the gingerbread animation, I don't think the human race can survive 100 deleterious mutatons per new born human.

Zachriel: Perhaps not.

Perhaps not? So does that mean that I could be right?

Do those models predict that selection will cause a net decrease in the harmfuls over time?

Your argument is unfounded. A clear quantitative answer may not be available

No it is not unfounded. And if you are understanding the problem, you will understand my claim is not unfounded.

You are not understanding the problem.

If every new born human has 100 novel harmful mutations, on what grounds can it be purged? Synergistic Epistasis cannot result in the net removal of harmfuls. No mechanism of selection can remove them because everyone is damaged!!!!

Take 10 people, 100 people,….6 billion people….

Who do you kill off, and who do you let survive? There will not be one who does not have a harfmul mutation given the premise that all have introduced harmful novelty.

It is your understanding that is not correct.

Most of which have no phenotypic effect.

No phenotypic effect immediately, but that only makes the problem worse since seleciton can't arrest it immediately and the damage gets passed on and then accumulates until it is to late to deal with.

Professor Williamson explains: 'It isn't so much that the number of people affected are going up it's more that the number of diseases that we recognise is increasing,"

Granted that is what he thinks, but some things to note.

The detection is of interest, and further the diseases are affecting only a handful of kids.

If it is found only in a hand ful of kids what does that mean?

If the disease has been around a long time, it only demonstrates selection doesn't do a good job weeding it out.

If the disease has been around recently, then it indicates they are new (as suggested by the low number of kids that have it).

In either case, selection isn't arresting the problem. And as I said, because of the interest in heritable diseases and the potential for cheap sequencing, we will be able to track the emergence and persistence of single nucleotide polymorphisms. The article is representative of the medical community being able to track and identify genetic diseases. If you were a bit more keen, you would have deduced that the article was not quite as irrelevant as you supposed.

(Nachman is the name of your gingerbread animation.)

For good reason. I think I was the one who first referenced the paper in the thread, not you.

Other Problems for Human Evolution

Nachman writes:

The high deleterious mutation rate in humans presents a paradox

Using conservative calculations of the proportion of the genome subject to purifying selection, we estimate that the genomic deleterious mutation rate (U) is at least 3. This high rate is difficult to reconcile with multiplicative fitness effects of individual mutations and suggests that synergistic epistasis among harmful mutations may be common.
….
For U = 3, the average fitness is reduced to 0.05, or put differently, each female would need to produce 40 offspring for 2 to survive and maintain the population at constant size. This assumes that all mortality is due to selection and so the actual number of offspring required to maintain a constant population size is probably higher. The problem can be mitigated somewhat by soft selection (WALLACE 1991 ) or by selection early in development (e.g., in utero). However, many mutations are unconditionally deleterious and it is improbable that the reproductive potential on average for human females can approach 40 zygotes. This problem can be overcome if most deleterious mutations exhibit synergistic epistasis; that is, if each additional mutation leads to a larger decrease in relative fitness (KONDRASHOV 1995 ; CROW 1997 ; EYRE-WALKER and KEIGHTLEY 1999 ). In the extreme, this gives rise to truncation selection in which all individuals carrying more than a threshold number of mutations are eliminated from the population. While extreme truncation selection seems unrealistic, the results presented here indicate that some form of positive epistasis among deleterious mutations is likely.

Do you recall the "re-normalization fix" I mentioned earlier? What does the bolded portion say to you, Zach. How do you misinterpret it?

For U = 3, the average fitness is reduced to 0.05, or put differently, each female would need to produce 40 offspring for 2 to survive and maintain the population at constant size. This assumes that all mortality is due to selection

Translation: the harmfuls are never removed from the population unless we have some individuals with NO new harmfuls AND they are the only ones that survive (an unrealistic conclusion). Why is that? Because if everyone has a new harmful, the harmfuls will accumulate and never be purged. That inference is not lost upon Nachman and Crowell, but it is lost upon you.

Comment by Salvador T. Cordova — November 12, 2009 @ 10:38 am

Zachriel Says:
November 12th, 2009 at 11:19 am
Salvador T. Cordova: Perhaps not? So does that mean that I could be right?

Of course. Do you not understand what it means for an argument to unfounded? It means the argument is flawed regardless of whether the result is wrong, whether you stumbled on the right answer, or whether you know the right answer, but can't explain how you arrived at it.

Salvador T. Cordova: Do those models predict that selection will cause a net decrease in the harmfuls over time?

As I indicated multiple times, it depends on a number of factors, including effective population size, number of offspring, mutation rate, ratio of beneficial-to-deleterious mutations, and variance in each of these.

Salvador T. Cordova: And if you are understanding the problem, you will understand my claim is not unfounded.

Is this a correct restatement? Your gingerbread model indicates that every child will be a mutant, and as the vast majority of those mutations will be deleterious, your model projects ever-declining fitness.

Salvador T. Cordova: No mechanism of selection can remove them because everyone is damaged!!!!

And this is why I say your argument is unfounded. Because you make overly broad claims. You haven't accounted for all the various mechanisms or parameters.

Using conservative calculations of the proportion of the genome subject to purifying selection, we estimate that the genomic deleterious mutation rate (U) is at least 3.

So you are aware of the estimate being 3, but you keep arguing 100 anyway.

While extreme truncation selection seems unrealistic, the results presented here indicate that some form of positive epistasis among deleterious mutations is likely.

Yes, I can bold too.

This problem can be overcome if most deleterious mutations exhibit synergistic epistasis

Your own cited expert doesn't see this as an unsoluable problem.

Keep in mind how close to the margin this is. We're talking an order of magnitude on fecundity and less than that on the rate of deleterious mutations. Life will tend to maximize evolutionary flexibility, so we expect it to move towards the edge. And that ignores positive epistasis, as well as recombination which reduces the disequilibrium induced by epistasis.

Instead of taking Nachman as a starting point, it apparently confirms your preconceptions to which you adhere. More recent research has offered many avenues to explain the so-called paradox.

Azevedo et al., Sexual reproduction selects for robustness and negative epistasis in artificial gene networks, Nature 2006.

Rice, Requisite mutational load, pathway epistasis, and deterministic mutation accumulation in sexual versus asexual populations, Genetica 2006.

Comment by Zachriel — November 12, 2009 @ 11:19 am

Salvador T. Cordova Says:
November 12th, 2009 at 11:32 am
Zachriel:

As I indicated multiple times, it depends on a number of factors, including effective population size, number of offspring, mutation rate, ratio of beneficial-to-deleterious mutations, and variance in each of these.

No it does not. If every new born has a novel harmful,, with respect to the basic premise that there will be a net increase in harmfuls per individual: the population size is irrelevant, the number of offspring is irrelevent, the beneficial-to-deleterious is irrelevant. We call these factors moot points!

The mutation rate (except the harmful rate which is assumed is irrelevant), and the presumption of 1 harmful (in the animation) or the 100 harmfuls (my claim) assumes that the variance from the mean still leaves 100 harmful.

So you've only repeated your distortions and minsinterpretations and misunderstandings of the scenario that I described.

Comment by Salvador T. Cordova — November 12, 2009 @ 11:32 am

Salvador T. Cordova Says:
November 12th, 2009 at 11:44 am
So you are aware of the estimate being 3, but you keep arguing 100 anyway.

The U=3 estimate was based on Ka/Ks ratios. That was in 2000. In 2005 that notion was discredited.

http://www.uchospitals.edu/news/2005/20050607-kaks.html

You clearly are not up-to-date on the current literature.

The estimate of 300 is based on empirical research not backfitted evolutionary theory. The citations are in Sanford's book.

By the way, I've mentioned illumina and solexa technology here at TT over the last year and UD in 2006.

Solexa was referenced here:

http://www.cell.com/current-biology/abstract/S0960-9822(09)01454-7

Understanding the key process of human mutation is important for many aspects of medical genetics and human evolution. In the past, estimates of mutation rates have generally been inferred from phenotypic observations or comparisons of homologous sequences among closely related species [1,2,3]. Here, we apply new sequencing technology to measure directly one mutation rate, that of base substitutions on the human Y chromosome. The Y chromosomes of two individuals separated by 13 generations were flow sorted and sequenced by Illumina (Solexa) paired-end sequencing to an average depth of 11× or 20×, respectively [4]. Candidate mutations were further examined by capillary sequencing in cell-line and blood DNA from the donors and additional family members. Twelve mutations were confirmed in ∼10.15 Mb; eight of these had occurred in vitro and four in vivo. The latter could be placed in different positions on the pedigree and led to a mutation-rate measurement of 3.0 × 10−8 mutations/nucleotide/generation (95% CI: 8.9 × 10−9–7.0 × 10−8),

What is lost in all this is that there is almost complete absence of purifying selection! If 90% of the genome is functional (as Sternberg reported), then that means 90% of the new mutations resulted in loss of function. Ergo, there has been un-arrested deterioration.

Comment by Salvador T. Cordova — November 12, 2009 @ 11:44 am

Salvador T. Cordova Says:
November 12th, 2009 at 12:40 pm
3.0 × 10−8 mutations/nucleotide/generation

Human genome 4 giga base pairs, at least 90% believed to be functional.

Hmm:

4 billion * 3 3.0 × 10−8 mutations/nucleotide/generation * 90% = 108

At the very least, it means, selection can't even detect or correct 108 new dysfunctional mutations per generation. On what grounds then can we suppose selection could have incorporated these mutations into the population in the first place?

Comment by Salvador T. Cordova — November 12, 2009 @ 12:40 pm

Mutations, fitness and more - Telic Thoughts Says:
November 12th, 2009 at 1:31 pm
[...] TT commenters, Zachriel and Salvador Cordova have an interesting exchange ongoing in the open thread. Salvador initiated the discussion with this comment. In one of his comments Zachriel mentioned the [...]

Pingback by Mutations, fitness and more - Telic Thoughts — November 12, 2009 @ 1:31 pm

Zachriel Says:
November 12th, 2009 at 1:43 pm
Salvador T. Cordova: If every new born has a novel harmful,, with respect to the basic premise that there will be a net increase in harmfuls per individual: the population size is irrelevant, the number of offspring is irrelevent, the beneficial-to-deleterious is irrelevant. We call these factors moot points!

Consider a population that randomly mates and each female produces a large number of children. And every child will experience a single mutation at birth. Assume strong selection in that the mutation is always fatal when homozygous, but of no consequence when heterozygous or nullizygous. The parents are heterozygous.

A) A quarter of the children will be stillborn. B) Half the children will have a recessive gene. C) And a quarter will be born with no mutant gene at all. Now, every child will now experience the inevitable mutation. Half of B) will die and all of C) will be become heterozygous, just like their parents. The result is that the offspring population has increased and yet has the same genetic composition as their parents.

Of course the actual situation is more complex. We're dealing with various shades of benefit or detriment, as well as other mechanisms, such as synergistic epistasis. But it does show that your argument is not correct. The parameters do matter.

Azevedo et al., Sexual reproduction selects for robustness and negative epistasis in artificial gene networks, Nature 2006.

Rice, Requisite mutational load, pathway epistasis, and deterministic mutation accumulation in sexual versus asexual populations, Genetica 2006.

Salvador T. Cordova: If 90% of the genome is functional (as Sternberg reported),

What does that mean "Sternberg reported?"

Comment by Zachriel — November 12, 2009 @ 1:43 pm

Zachriel Says:
November 12th, 2009 at 1:52 pm
Salvador T. Cordova:
http://www.uchospitals.edu/news/2005/20050607-kaks.html

"We've discovered a striking phenomenon that challenges a paradigm of molecular evolution that has been around for several decades," said lead author

Bruce Lahn, PhD, assistant professor of genetics at the University of Chicago and Howard Hughes Medical Institute investigator.

Is that this Bruce Lahn?
http://www.sciencedaily.com/releases/2005/09/050909221043.htm

"Our studies indicate that the trend that is the defining characteristic of human evolution–the growth of brain size and complexity–is likely still going on," said lead researcher for both papers

Bruce Lahn, PhD, assistant professor of human genetics at the University of Chicago and an investigator at the Howard Hughes Medical Institute.

Comment by Zachriel — November 12, 2009 @ 1:52 pm

fifth monarchy man Says:
November 17th, 2009 at 6:45 pm
Hey Zach,

How does a trait like this fit in the nested hierarchy?

peace

Comment by fifth monarchy man — November 17, 2009 @ 6:45 pm

Zachriel Says:
November 17th, 2009 at 8:03 pm
fifth monarchy man: How does a trait like this fit in the nested hierarchy?

Sort of like asking how "wings" of birds and bats fit into the nested hierarchy. Even though the bones in Myotragus show rings indicating variable rates of growth, they're still mammalian bones. Myotragus is highly derived, but definitely a bovid, as confirmed by the molecular evidence. The similar adaptation is due to the similar conditions.

Köhler and Moyà-Solà, Physiological and life history strategies of a fossil large mammal in a resource-limited environment, PNAS 2009:

Our present study, hence, provides evidence that in energy-poor environments where reptiles usually replace mammals, selection for energy saving may be so imperious that mammals may revert to some ectotherm-like state that includes both physiological and developmental plasticity… Myotragus did not survive the arrival of a major predator, Homo sapiens, some 3,000 years ago.

Comment by Zachriel — November 17, 2009 @ 8:03 pm

fifth monarchy man Says:
November 17th, 2009 at 8:26 pm
The similar adaptation is due to the similar conditions.

So how exactly does one determine when similarity in a trait is due to this reason rather than common ancestry with out presupposing common ancestry from the get go?

Why do the vast majority of mammals in similar conditions not devolp this trait?

Myotragus show rings indicating variable rates of growth, they're still mammalian bones.

How do we know that they are not a transitional feature between reptile and mammal like a monotreme egg? Again with out presupposing the tree right out of the box.

I'm just trying to get a handel on your thought process. Its all I can do since you have proven that honest discussion is impossible in your case.

peace

Comment by fifth monarchy man — November 17, 2009 @ 8:26 pm

Bradford Says:
November 17th, 2009 at 9:09 pm
Obama wins no concessions from China on points at issue

Obama has little leverage over China, in part because the U.S. depends on the Chinese to finance the U.S. government's growing debt, and because of the perception in China, which for years was an economic nonentity, that the U.S. is troubled and China is ascendant.

This is what happens when the government spends much more money than it can afford. It puts the USA into a position of depending on creditors i.e. the Chinese.

This is a wake up call for the people of reason. All the apologies and false humility get us nothing. No concessions in Europe or Asia. None from Iran. Rock stars deliver on a musical stage. Not on the international stage.

Comment by Bradford — November 17, 2009 @ 9:09 pm

Zachriel Says:
November 18th, 2009 at 8:36 am
fifth monarchy man: So how exactly does one determine when similarity in a trait is due to this reason rather than common ancestry with out presupposing common ancestry from the get go?

The discussion of the nested hierarchy on this forum is like Harrison Bergeron. There's too much noise to continue the thought.

1) 0123456789000a 2) 0123456789200b 3) 9726283492234B

Which two match? Does the fact that 2) and 3) both share the b in the last position change your opinion? If you look more closely, the two b's are actually different. One's a capital letter.

Now consider mammals and birds, and try to place bats. Wow, the bats have mammaries, three ear bones, hair, neocortex, teeth, bellows lungs. All sorts of features found in mammals. But bats have wings like birds. Hmm. If we look more closely, though, we see that bird wings are made of feathers attached to the arm, while bat wings are skin stretched across extended phalanges. Bats are mammals.

Finally, let us consider Myotragus. Well, you must admit it groups with other chordates, indeed gnathostomes, amniotes, tetrapods. (Or do we really have to start at the beginning. It's the nested hierarchy!) Reptiles have several bones in the lower jaw, and more or less conical teeth; while mammals have a single lower jaw bone and specialized teeth. In reptiles, the head attaches at a single point; while in mammals, the attachment is double-faced. The ilium in mammals allow for an upright stance. And so on. Myotragus is an Artiodactyl, and has a specialized ankle bone, the astragalus, which has a double-pulley structure. And finally, its a bovid with four toes and horns.

Now, this is the key. If we find a astragalus with the double-pulley structrure, then we can predict many other features of the organism. That it has vertebrae. That it has a cranium. That is has a jaw. That the lower jaw is a single bone. We can't be absolutely sure, of course. All species are derived. But there is little doubt that the ankle bone alone is sufficient, due to the vast support for the nested hierarchy, to say the organism has vertebrae, cranium, jaw, etc.

Comment by Zachriel — November 18, 2009 @ 8:36 am

Zachriel Says:
November 18th, 2009 at 8:48 am
Let me add that we are only pointing to the *observed* nested hierarchy, and not to Common Descent. The vast amount of data supporting the nested hierarchy across most taxa allows us to make testable, empirical predictions.

Comment by Zachriel — November 18, 2009 @ 8:48 am

ID guy Says:
November 18th, 2009 at 8:54 am
Zachriel:
The discussion of the nested hierarchy on this forum is like Harrison Bergeron. There's too much noise to continue the thought.

The problem with discussing nested hierarchies with Zachriel is that he doesn't understand the concept and thinks his ignorance is knowledge.

However it does appear that you have finally learned that nested hierarchies are built with defined characteristics and that descent is not a defining characteristic.

Now if we take a look at reptile to mammal transition-

Reptiles are cold blooded. That is a defining characteristic of reptiles.

In order for there to be a nested hierarchy based on descent, mammals would have to be both cold and warm blooded.

But seeing that mammals are just warm blooded the containment required by nested hierarchies is broken/ violated.

Now, this is key because if one cannot grasp that basic concept then one cannot grasp the concept of nested hierarchies.

Comment by ID guy — November 18, 2009 @ 8:54 am

ID guy Says:
November 18th, 2009 at 8:56 am
Zachriel:
Let me add that we are only pointing to the *observed* nested hierarchy, and not to Common Descent. The vast amount of data supporting the nested hierarchy across most taxa allows us to make testable, empirical predictions.

Predictions based on what? Obviously not Common Descent.

Comment by ID guy — November 18, 2009 @ 8:56 am

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