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It is some time since I have posted this, so I thought it was time for

another outing. So, once again, we have ...

rossum

The Evolution of Boojmase

=========================

Creationists often talk about the impossible odds of evolution

producing a working protein. When they, rarely, show their

calculatins, they always have the same error in them. Evolutin is a

process including both random mutation and natural selection. The

creationist's models invarialy omit the natural selection part, and

only include the random mutation bit, what they often describe as a

"tornado in a junkyard", following Hoyle. That model is incorrect.

Using a correct model gives very different results.

Their naive "protein probability" calculation uses a very crude model

of evolution, basically it assumes the evolution of the whole protein

in a single large step. This gives a chance of one in 20^100 for a

protein with 100 amino acids. 20^100 comes to 1.27 x 10^131 so the

chance of the protein appearing in one step is 1 in 1.27 x 10^131.

The usual calculation is then to halve this number and say that in a

species that reproduces annually the protein is only likely to appear

after 6.35 x 10^130 years at 50% probability, which is far longer than

the age of the earth.

The model implied in the naive calculation is not the model used by

evolution. Under evolution small changes arise randomly, and may be

beneficial or deleterious. Once arisen they are selected very

non-randomly with the deleterious changes disappearing and the

beneficial changes spreading through the population. This has the

effect of spreading out the development of the protein so that instead

of one very large and unlikely jump there are a lot of smaller jumps

which are individually more likely. It also allows for the ratcheting

effect of natural selection, whereby any deleterious mutations tend to

disappear from the population and any beneficial mutations tend to

spread through the population and still be around when the next

mutation comes along.

Using a better model gives a time to evolve a protein with 100 amino

acids of just over two million years. The evolutionary model given

below for the evolution of boojumase is more complex than the naive

model, so it will need more complex calculations.

1 The Scenario

==============

Momerathius vulgaris, the common Mome Rath, is a sessile marine filter

feeder. It lives for one year, reproduces and dies. Its normal food

is a protist, Snarkius snarkius, the snark. However a proportion of

snarks are actually boojums, Snarkius boojum. Boojums have a

different cell wall, so are indigestible, most passing through the

Mome Rath's gut undigested. If there are too many boojums in the Mome

Rath's diet then it will softly and suddenly vanish away.

Mome Raths have an enzyme to digest the cell walls of snarks:

snarkase. The gene for snarkase is duplicated in the Mome Rath's

genome. This means that the second copy of the snarkase gene, called

"snk2", is available to evolve into a new gene to code for boojumase,

which will allow the Mome Rath to digest boojums as well. Any Mome

Rath possessing even a partially effective boojumase will have an

advantage in that it will have more food available and will have a

reduced chance of softly and suddenly vanishing away.

I will calculate the likely time to evolve a gene for boojumase from

the second copy of the snarkase gene. The answer turns out to be

2,096,000 years, a long time but certainly not impossible. This

figure is confirmed to within 2% by computer modelling.

2 Assumptions

=============

1 The population of Mome Raths is stable at about 10 million

individuals. Predation limits the population so the effectiveness of

boojumase is not a factor.

2 Both snarkase and boojumase contain 100 amino acids.

3 In a boojumase there is only one effective amino acid allowed in

each of the 100 positions, any of the nineteen other amino acids is

ineffective in that position.

4 Snarkase and boojumase are very different so their initial match is

just 5% (1 in 20). This is the level of matching expected from any

two random series of 100 amino acids.

5 I will only deal with mutations that have a real effect on the snk2

gene, called "significant mutations". This effect may be good or bad,

but there must be a real effect. Neutral mutations are ignored,

including replacing one ineffective amino acid with a different, but

still ineffective, amino acid in a given position. Mutations

affecting other genes are also ignored.

6 Every four thousand years there is a significant mutation in the

snk2 gene of one Mome Rath in the population of ten million. The

resulting change is random and may be good or bad. In each of the 100

positions replacing an ineffective amino acid with an effective amino

acid is good. Replacing an effective amino acid with an ineffective

one is bad. For the purposes of this model any beneficial mutation

that appears and then gets eaten by a predator or otherwise fails to

reproduce is ignored.

7 The effectiveness of a boojumase at digesting boojums is equal to

the percentage of effective amino acids it contains. Thus since

normal snarkase has 5% effective amino acids it can digest 5% of

boojums during their passage through the mome rath's gut. A boojumase

with 20 effective amino acids would be 20% effective and would digest

20% of boojums and so forth.

8 Each 1% of increased effectiveness of boojumase gives a Mome Rath a

1% advantage in reproduction. Similarly a 1% decrease in

effectiveness will give a 1% decrease in the effectiveness of

reproduction. This includes the effect of the changed probability of

the Mome Rath softly and suddenly vanishing away.

3 Preliminary Calculations

==========================

3.1 Beneficial Mutations

------------------------

First I will look at the spread of beneficial mutations. On average

each Mome Rath will reproduce exactly one Mome Rath that survives to

maturity and reproduces - this keeps the population stable. A Mome

Rath with a single mutation for a better boojumase will reproduce 1.01

Mome Raths (1% better than average), while one with a mutation for a

worse boojumase will only reproduce 0.99 Mome Raths (1% worse than

average). Better and worse will be relative, since the population

will stay at 10 million Mome Raths as the improved boojumase evolves.

How long will it take a single beneficial mutation to spread through

the population?

Initially the number of Mome Raths with the beneficial mutation will

increase from the original single individual as the powers of 1.01.

After 1551 years they will form half of the population, about 5

million (1.01 ^ 1551 = 5,040,234). From this point they will be the

normal population while those without the mutation will be the

minority. The minority will decrease as the powers of 0.99. After a

further 1604 years those without the mutation will be extinct, less

than half an individual in the population: 5,000,000 x (0.99 ^ 1604) =

0.4986802).

This means that it will take about 1551 + 1604 = 3155 years to replace

a population with the old snk2 gene with a new population with the new

improved snk2 gene.

3.2 Deleterious Mutations

-------------------------

If a deleterious mutation occurs then it will decrease as powers of

0.99 since it will be 1% less efficient at reproducing. From an

initial population of one single individual it will fall below 0.5 in

69 years (1 x 0.99 ^ 69 = 0.499837). The deleterious mutation will be

eliminated by natural selection in less than 100 years.

3.3 Mutation Rates

------------------

I have assumed one significant mutation every four thousand years. Is

this a reasonable assumption? The mutation rate for mammals is about

3 x 10 ^ -8 mutations per base pair per generation. Applying this

rate to M. vulgaris we would expect about 3 x 10 ^ -6 mutations in the

100 base pair snk2 gene per individual. With 10 million individuals

in the population this is 3 x 10 ^ -6 x 10 ^ 7 = 30 mutations in the

snk2 gene over the whole population in each generation. Naturally,

many of these mutations will be neutral. Over 4000 years there will

be 4000 x 30 = 120000 mutations in the snk2 gene over the whole

population.

From this it would appear that the rate of one significant mutation

every 4000 years is probably an underestimate. Nevertheless I will

retain it in order to avoid overlapping mutations and so simplify the

calculations. This means that the time calculated will be longer than

it would be if a more realistic rate for significant mutations was

used.

4 Mutate!

=========

4.1 The First Three Mutations

-----------------------------

Every four thousand years there is a significant mutation in the snk2

gene of one individual Mome Rath. Since the initial snarkase has 5%

effective amino acids, the first significant mutation will have a 95%

chance of being beneficial; switching an ineffective amino acid to an

effective one. It will have a 5% chance of being deleterious;

switching an effective amino acid to an ineffective one.

Deleterious mutations will disappear in 69 years, so they will be gone

before the next significant mutation in 4,000 years. Beneficial

mutations spread through the entire population in 3,155 years, so the

entire population will have the improved boojumase before the next

significant mutation. This means that significant mutations will not

overlap.

Deleterious mutation will disappear and so will not change the

probabilities for the next mutation in 4,000 years; the boojumase will

be unchanged. Beneficial mutations will be preserved and so will

increase the probability of a subsequent deleterious mutation by 1%

and reduce the probability of a beneficial mutation in 4,000 years

time. Boojumase will now be 1% more effective than before.

Drawing up the first three mutations in tables (best in a monospaced

font like Courier):

Mutation 1 (Year 4000) Mutation 2 (8000) Mutation 3 (12000)

D = 5% DD = 5% x 5% DDD = 5% x 5% x 5%

B = 95% DB = 5% x 95% DDB = 5% x 5% x 95%

BD = 95% x 6% DBD = 5% x 95% x 6%

BB = 95% x 94% DBB = 5% x 95% x 94%

BDD = 95% x 6% x 6%

BDB = 95% x 6% x 94%

BBD = 95% x 94% x 7%

BBB = 95% x 94% x 93%

Here D is a deleterious mutation and B is a beneficial mutation.

Taking an example, BBD in the seventh row of the third table, there is

a beneficial mutation followed by another beneficial mutation followed

by a deleterious mutation. The first beneficial mutation has a

probability of 95%, the second beneficial mutation only has a

probability of 94% since the boojumase now has 6 effective amino acids

and 94 ineffective ones as it was improved by the first beneficial

mutation. The probability of the final deleterious mutation is 7%

since there are seven effective amino acids in the boojumase after two

beneficial mutations.

4.2 Average Expected Effectiveness

----------------------------------

Tracing this through many mutations will result in huge tables: 2 ^

100 rows after 100 mutations. In order to proceed I am going to

simplify the calculation by working out a single "Average Expected

Effectiveness" (AEE) for the effectiveness of the boojumase. Doing

some more calculations on the table for the third mutation gives:

Prob. Effect. P x E

DDD 0.0125% 5% 0.000625%

DDB 0.2375% 6% 0.014250%

DBD 0.2850% 6% 0.017100%

DBB 4.4650% 7% 0.312550%

BDD 0.3420% 6% 0.020520%

BDB 5.3580% 7% 0.375060%

BBD 6.2510% 7% 0.437570%

BBB 83.0490% 8% 6.643920%

-------- ---------

100.0000% 7.821595% = AEE

Here the "Prob." column is the probability of that particular outcome

for the three mutations; for example the probability of DBD is 5% x

95% x 6% = 0.2850%. The sum of the probabilities is 100% as a check

on the calculation. The "Effect." column is the effectiveness of the

boojumase after the mutations; start at 5% and add 1% for each B, so

DDD is still at 5% effectiveness while BBB is at the maximum possible

8% effectiveness after three beneficial mutations. The "P x E" column

is the previous two columns multiplied together and adjusted to a

percentage. Each entry is the proportion of the effectiveness that

this row contributes to the overall expected effectiveness of the

boojumase. The sum of this column is the "average expected

effectiveness" (AEE) that I wish to calculate: 7.82 to two decimal

places.

4.3 The Fourth Mutation

-----------------------

Coming into the fourth mutation the average expected effectiveness

(AEE) is 7.82. This gives a 7.82% chance of a deleterious mutation

and a (100.00 - 7.82) = 92.18% chance of a beneficial mutation. The

table looks like:

Mutation 4 (16000) Initial AEE = 7.82%

Prob. Effect. P x E

D 7.82% 7.82% 0.61%

B 92.18% 8.82% 8.13%

------- -----

100.00% 8.74% = new AEE

The probability of a deleterious mutation, D, is the AEE, 7.82. The

probability of a beneficial mutation, B, is (100 - AEE), 92.18%. The

effectiveness of the boojumase after a deleterious mutation is

unchanged, the AEE, 7.82%. The effectiveness of the boojumase after a

beneficial mutation is increased by 1%, (AEE + 1), 8.82%. The P x E

column has AEE x AEE / 100 in the D row and (100 - AEE) x (AEE + 1) /

100 in the B row. In each case the "/ 100" is to get the P x E column

back into a percentage. The new AEE is the sum of these two values:

(AEE x AEE / 100) + ((100 - AEE) x (AEE + 1) / 100). This is the new

value of the AEE to go forward to the next mutation.

4.4 The Fifth Mutation

----------------------

From the discussion of the fourth mutation there is a formula for

calculating the AEE after fifth mutation. The formula is:

New AEE = (AEE x AEE / 100) + ((100 - AEE) x (AEE + 1) / 100)

This can be simplified to:

New AEE = ((99 x AEE) + 100) / 100

Putting the AEE of 8.74 coming into the fifth mutation into the

formula gives 9.65 to two decimal places for the AEE after the fifth

mutation.

4.5 And so on...

----------------

The simplified formula from section 4.4 can be used to step from

mutation to mutation. The calculation is best shown in a table. Rows

are missed out purely for reasons of space. It is simple to set up

the whole thing on a spreadsheet.

Year Mutation AEE after

12000 3 7.82%

16000 4 8.74%

20000 5 9.65%

40000 10 14.08%

80000 20 22.30%

100000 25 26.11%

200000 50 42.52%

500000 125 72.95%

800000 200 87.27%

1000000 250 92.30%

2000000 500 99.38%

2096000 524 99.51%

This shows that after a million years of evolution and 250 significant

mutations M. vulgaris has a snk2 gene that codes for a boojumase that

is on average 92% effective. 92 of the hundred amino acids in the

boojumase are effective, on average only eight are ineffective. After

two million years 99 of the hundred amino acids are effective with an

average of one ineffective amino acid.

The table also shows that as the boojumase becomes more effective,

random mutations are more likely to be deleterious, so it takes longer

between beneficial mutations.

5 Result

========

After an average of 2,096,000 years and 524 significant mutations the

Mome Raths have evolved the most effective boojumase possible as there

is less than half an amino acid that is ineffective on average. The

Mome Raths have adapted to an environment containing boojums and will

not softly and suddenly vanish away.

This average figure of 2,096,000 years to evolve a protein with 100

amino acids compares with the 6.35 x 10^130 years calculated from the

less realistic naive model that failed to account for the non-random

element of natural selection.

6 Computer Modelling

====================

Putting this model into a computer program and running it through to

the evolution of a 99.5% effective boojumase a million times gave the

results:

Mean Mutations Std Deviation

513.74 125.97

Running the program three more times, each with a million repetitions

gave:

Mean Mutations Std Deviation

513.65 125.89

513.71 125.79

513.70 125.86

This seems to indicate that the calculations above are a little

pessimistic, and the average should be 514 mutations, taking 2,056,000

years instead of 524 mutations taking 2,096,000 years. The error is

less than two percent. No doubt a better mathematician or

statistician than me could explain the discrepancy.

7 The Boojumase Model

=====================

This is a simple model, deliberately so in order to simplify the

calculations. However it is more complex and closer to the real

situation than the model implied by the naive probability calculation.

The naive model covers the random nature of mutations but it does not

include either the highly non-random process of natural selection or

the ratcheting effect of small changes over the generations in a

population and so gives a misleading result. The boojumase model by

including random mutations, the non-random element of natural

selection and the ratchet effect gives a less misleading result.

The boojumase model is intended as a learning aid. For that reason it

is simplified to remove all calculus and more advanced mathematics.

It is intended for an interested lay audience, not for publication in

Science or Nature.

I have deliberately made life difficult for the model by starting with

the 5% random match between snarkase and boojumase, by allowing only

one amino acid to be effective at each position and by picking a long

interval between significant mutations. This is to avoid criticism

that the model is biased in favour of a short time to evolve the

protein; if anything the model is biased towards a long time to evolve

the protein.

The model is by no means perfect. Possible improvements to it are:

- To improve the calculation of the time taken to spread a beneficial

mutation through the whole population. I tried this myself and got a

figure of 3293 years; not different enough to warrant the extra

complexity and with no effect on the overall result as it is still

less than 4,000 years.

- To take into account sexual reproduction in the spreading of

beneficial mutations.

- Run the exact calculation of tables for more than three mutations

before switching to the AEE.

- Explain the transition from the exact tables to the AEE better than

I have in section 4.2.

- Allow mutations to overlap so a second significant mutation might

occur before the previous mutation has spread through the whole

population. This would allow a more realistic rate of significant

mutations.

- Look at mutation rates in real life and make a better assumption

for the interval between significant mutations. I picked 4000 years

purely to avoid complications with overlapping mutations.

Feel free to take up this model, clean it up and make it a better

reflection of reality. If you do so please bear in mind its purpose

and do not complicate it too much; remember the target audience.

8 Bibliography

==============

Lewis Carroll: Jabberwocky

Lewis Carroll: The Hunting of the Snark

another outing. So, once again, we have ...

rossum

The Evolution of Boojmase

=========================

Creationists often talk about the impossible odds of evolution

producing a working protein. When they, rarely, show their

calculatins, they always have the same error in them. Evolutin is a

process including both random mutation and natural selection. The

creationist's models invarialy omit the natural selection part, and

only include the random mutation bit, what they often describe as a

"tornado in a junkyard", following Hoyle. That model is incorrect.

Using a correct model gives very different results.

Their naive "protein probability" calculation uses a very crude model

of evolution, basically it assumes the evolution of the whole protein

in a single large step. This gives a chance of one in 20^100 for a

protein with 100 amino acids. 20^100 comes to 1.27 x 10^131 so the

chance of the protein appearing in one step is 1 in 1.27 x 10^131.

The usual calculation is then to halve this number and say that in a

species that reproduces annually the protein is only likely to appear

after 6.35 x 10^130 years at 50% probability, which is far longer than

the age of the earth.

The model implied in the naive calculation is not the model used by

evolution. Under evolution small changes arise randomly, and may be

beneficial or deleterious. Once arisen they are selected very

non-randomly with the deleterious changes disappearing and the

beneficial changes spreading through the population. This has the

effect of spreading out the development of the protein so that instead

of one very large and unlikely jump there are a lot of smaller jumps

which are individually more likely. It also allows for the ratcheting

effect of natural selection, whereby any deleterious mutations tend to

disappear from the population and any beneficial mutations tend to

spread through the population and still be around when the next

mutation comes along.

Using a better model gives a time to evolve a protein with 100 amino

acids of just over two million years. The evolutionary model given

below for the evolution of boojumase is more complex than the naive

model, so it will need more complex calculations.

1 The Scenario

==============

Momerathius vulgaris, the common Mome Rath, is a sessile marine filter

feeder. It lives for one year, reproduces and dies. Its normal food

is a protist, Snarkius snarkius, the snark. However a proportion of

snarks are actually boojums, Snarkius boojum. Boojums have a

different cell wall, so are indigestible, most passing through the

Mome Rath's gut undigested. If there are too many boojums in the Mome

Rath's diet then it will softly and suddenly vanish away.

Mome Raths have an enzyme to digest the cell walls of snarks:

snarkase. The gene for snarkase is duplicated in the Mome Rath's

genome. This means that the second copy of the snarkase gene, called

"snk2", is available to evolve into a new gene to code for boojumase,

which will allow the Mome Rath to digest boojums as well. Any Mome

Rath possessing even a partially effective boojumase will have an

advantage in that it will have more food available and will have a

reduced chance of softly and suddenly vanishing away.

I will calculate the likely time to evolve a gene for boojumase from

the second copy of the snarkase gene. The answer turns out to be

2,096,000 years, a long time but certainly not impossible. This

figure is confirmed to within 2% by computer modelling.

2 Assumptions

=============

1 The population of Mome Raths is stable at about 10 million

individuals. Predation limits the population so the effectiveness of

boojumase is not a factor.

2 Both snarkase and boojumase contain 100 amino acids.

3 In a boojumase there is only one effective amino acid allowed in

each of the 100 positions, any of the nineteen other amino acids is

ineffective in that position.

4 Snarkase and boojumase are very different so their initial match is

just 5% (1 in 20). This is the level of matching expected from any

two random series of 100 amino acids.

5 I will only deal with mutations that have a real effect on the snk2

gene, called "significant mutations". This effect may be good or bad,

but there must be a real effect. Neutral mutations are ignored,

including replacing one ineffective amino acid with a different, but

still ineffective, amino acid in a given position. Mutations

affecting other genes are also ignored.

6 Every four thousand years there is a significant mutation in the

snk2 gene of one Mome Rath in the population of ten million. The

resulting change is random and may be good or bad. In each of the 100

positions replacing an ineffective amino acid with an effective amino

acid is good. Replacing an effective amino acid with an ineffective

one is bad. For the purposes of this model any beneficial mutation

that appears and then gets eaten by a predator or otherwise fails to

reproduce is ignored.

7 The effectiveness of a boojumase at digesting boojums is equal to

the percentage of effective amino acids it contains. Thus since

normal snarkase has 5% effective amino acids it can digest 5% of

boojums during their passage through the mome rath's gut. A boojumase

with 20 effective amino acids would be 20% effective and would digest

20% of boojums and so forth.

8 Each 1% of increased effectiveness of boojumase gives a Mome Rath a

1% advantage in reproduction. Similarly a 1% decrease in

effectiveness will give a 1% decrease in the effectiveness of

reproduction. This includes the effect of the changed probability of

the Mome Rath softly and suddenly vanishing away.

3 Preliminary Calculations

==========================

3.1 Beneficial Mutations

------------------------

First I will look at the spread of beneficial mutations. On average

each Mome Rath will reproduce exactly one Mome Rath that survives to

maturity and reproduces - this keeps the population stable. A Mome

Rath with a single mutation for a better boojumase will reproduce 1.01

Mome Raths (1% better than average), while one with a mutation for a

worse boojumase will only reproduce 0.99 Mome Raths (1% worse than

average). Better and worse will be relative, since the population

will stay at 10 million Mome Raths as the improved boojumase evolves.

How long will it take a single beneficial mutation to spread through

the population?

Initially the number of Mome Raths with the beneficial mutation will

increase from the original single individual as the powers of 1.01.

After 1551 years they will form half of the population, about 5

million (1.01 ^ 1551 = 5,040,234). From this point they will be the

normal population while those without the mutation will be the

minority. The minority will decrease as the powers of 0.99. After a

further 1604 years those without the mutation will be extinct, less

than half an individual in the population: 5,000,000 x (0.99 ^ 1604) =

0.4986802).

This means that it will take about 1551 + 1604 = 3155 years to replace

a population with the old snk2 gene with a new population with the new

improved snk2 gene.

3.2 Deleterious Mutations

-------------------------

If a deleterious mutation occurs then it will decrease as powers of

0.99 since it will be 1% less efficient at reproducing. From an

initial population of one single individual it will fall below 0.5 in

69 years (1 x 0.99 ^ 69 = 0.499837). The deleterious mutation will be

eliminated by natural selection in less than 100 years.

3.3 Mutation Rates

------------------

I have assumed one significant mutation every four thousand years. Is

this a reasonable assumption? The mutation rate for mammals is about

3 x 10 ^ -8 mutations per base pair per generation. Applying this

rate to M. vulgaris we would expect about 3 x 10 ^ -6 mutations in the

100 base pair snk2 gene per individual. With 10 million individuals

in the population this is 3 x 10 ^ -6 x 10 ^ 7 = 30 mutations in the

snk2 gene over the whole population in each generation. Naturally,

many of these mutations will be neutral. Over 4000 years there will

be 4000 x 30 = 120000 mutations in the snk2 gene over the whole

population.

From this it would appear that the rate of one significant mutation

every 4000 years is probably an underestimate. Nevertheless I will

retain it in order to avoid overlapping mutations and so simplify the

calculations. This means that the time calculated will be longer than

it would be if a more realistic rate for significant mutations was

used.

4 Mutate!

=========

4.1 The First Three Mutations

-----------------------------

Every four thousand years there is a significant mutation in the snk2

gene of one individual Mome Rath. Since the initial snarkase has 5%

effective amino acids, the first significant mutation will have a 95%

chance of being beneficial; switching an ineffective amino acid to an

effective one. It will have a 5% chance of being deleterious;

switching an effective amino acid to an ineffective one.

Deleterious mutations will disappear in 69 years, so they will be gone

before the next significant mutation in 4,000 years. Beneficial

mutations spread through the entire population in 3,155 years, so the

entire population will have the improved boojumase before the next

significant mutation. This means that significant mutations will not

overlap.

Deleterious mutation will disappear and so will not change the

probabilities for the next mutation in 4,000 years; the boojumase will

be unchanged. Beneficial mutations will be preserved and so will

increase the probability of a subsequent deleterious mutation by 1%

and reduce the probability of a beneficial mutation in 4,000 years

time. Boojumase will now be 1% more effective than before.

Drawing up the first three mutations in tables (best in a monospaced

font like Courier):

Mutation 1 (Year 4000) Mutation 2 (8000) Mutation 3 (12000)

D = 5% DD = 5% x 5% DDD = 5% x 5% x 5%

B = 95% DB = 5% x 95% DDB = 5% x 5% x 95%

BD = 95% x 6% DBD = 5% x 95% x 6%

BB = 95% x 94% DBB = 5% x 95% x 94%

BDD = 95% x 6% x 6%

BDB = 95% x 6% x 94%

BBD = 95% x 94% x 7%

BBB = 95% x 94% x 93%

Here D is a deleterious mutation and B is a beneficial mutation.

Taking an example, BBD in the seventh row of the third table, there is

a beneficial mutation followed by another beneficial mutation followed

by a deleterious mutation. The first beneficial mutation has a

probability of 95%, the second beneficial mutation only has a

probability of 94% since the boojumase now has 6 effective amino acids

and 94 ineffective ones as it was improved by the first beneficial

mutation. The probability of the final deleterious mutation is 7%

since there are seven effective amino acids in the boojumase after two

beneficial mutations.

4.2 Average Expected Effectiveness

----------------------------------

Tracing this through many mutations will result in huge tables: 2 ^

100 rows after 100 mutations. In order to proceed I am going to

simplify the calculation by working out a single "Average Expected

Effectiveness" (AEE) for the effectiveness of the boojumase. Doing

some more calculations on the table for the third mutation gives:

Prob. Effect. P x E

DDD 0.0125% 5% 0.000625%

DDB 0.2375% 6% 0.014250%

DBD 0.2850% 6% 0.017100%

DBB 4.4650% 7% 0.312550%

BDD 0.3420% 6% 0.020520%

BDB 5.3580% 7% 0.375060%

BBD 6.2510% 7% 0.437570%

BBB 83.0490% 8% 6.643920%

-------- ---------

100.0000% 7.821595% = AEE

Here the "Prob." column is the probability of that particular outcome

for the three mutations; for example the probability of DBD is 5% x

95% x 6% = 0.2850%. The sum of the probabilities is 100% as a check

on the calculation. The "Effect." column is the effectiveness of the

boojumase after the mutations; start at 5% and add 1% for each B, so

DDD is still at 5% effectiveness while BBB is at the maximum possible

8% effectiveness after three beneficial mutations. The "P x E" column

is the previous two columns multiplied together and adjusted to a

percentage. Each entry is the proportion of the effectiveness that

this row contributes to the overall expected effectiveness of the

boojumase. The sum of this column is the "average expected

effectiveness" (AEE) that I wish to calculate: 7.82 to two decimal

places.

4.3 The Fourth Mutation

-----------------------

Coming into the fourth mutation the average expected effectiveness

(AEE) is 7.82. This gives a 7.82% chance of a deleterious mutation

and a (100.00 - 7.82) = 92.18% chance of a beneficial mutation. The

table looks like:

Mutation 4 (16000) Initial AEE = 7.82%

Prob. Effect. P x E

D 7.82% 7.82% 0.61%

B 92.18% 8.82% 8.13%

------- -----

100.00% 8.74% = new AEE

The probability of a deleterious mutation, D, is the AEE, 7.82. The

probability of a beneficial mutation, B, is (100 - AEE), 92.18%. The

effectiveness of the boojumase after a deleterious mutation is

unchanged, the AEE, 7.82%. The effectiveness of the boojumase after a

beneficial mutation is increased by 1%, (AEE + 1), 8.82%. The P x E

column has AEE x AEE / 100 in the D row and (100 - AEE) x (AEE + 1) /

100 in the B row. In each case the "/ 100" is to get the P x E column

back into a percentage. The new AEE is the sum of these two values:

(AEE x AEE / 100) + ((100 - AEE) x (AEE + 1) / 100). This is the new

value of the AEE to go forward to the next mutation.

4.4 The Fifth Mutation

----------------------

From the discussion of the fourth mutation there is a formula for

calculating the AEE after fifth mutation. The formula is:

New AEE = (AEE x AEE / 100) + ((100 - AEE) x (AEE + 1) / 100)

This can be simplified to:

New AEE = ((99 x AEE) + 100) / 100

Putting the AEE of 8.74 coming into the fifth mutation into the

formula gives 9.65 to two decimal places for the AEE after the fifth

mutation.

4.5 And so on...

----------------

The simplified formula from section 4.4 can be used to step from

mutation to mutation. The calculation is best shown in a table. Rows

are missed out purely for reasons of space. It is simple to set up

the whole thing on a spreadsheet.

Year Mutation AEE after

12000 3 7.82%

16000 4 8.74%

20000 5 9.65%

40000 10 14.08%

80000 20 22.30%

100000 25 26.11%

200000 50 42.52%

500000 125 72.95%

800000 200 87.27%

1000000 250 92.30%

2000000 500 99.38%

2096000 524 99.51%

This shows that after a million years of evolution and 250 significant

mutations M. vulgaris has a snk2 gene that codes for a boojumase that

is on average 92% effective. 92 of the hundred amino acids in the

boojumase are effective, on average only eight are ineffective. After

two million years 99 of the hundred amino acids are effective with an

average of one ineffective amino acid.

The table also shows that as the boojumase becomes more effective,

random mutations are more likely to be deleterious, so it takes longer

between beneficial mutations.

5 Result

========

After an average of 2,096,000 years and 524 significant mutations the

Mome Raths have evolved the most effective boojumase possible as there

is less than half an amino acid that is ineffective on average. The

Mome Raths have adapted to an environment containing boojums and will

not softly and suddenly vanish away.

This average figure of 2,096,000 years to evolve a protein with 100

amino acids compares with the 6.35 x 10^130 years calculated from the

less realistic naive model that failed to account for the non-random

element of natural selection.

6 Computer Modelling

====================

Putting this model into a computer program and running it through to

the evolution of a 99.5% effective boojumase a million times gave the

results:

Mean Mutations Std Deviation

513.74 125.97

Running the program three more times, each with a million repetitions

gave:

Mean Mutations Std Deviation

513.65 125.89

513.71 125.79

513.70 125.86

This seems to indicate that the calculations above are a little

pessimistic, and the average should be 514 mutations, taking 2,056,000

years instead of 524 mutations taking 2,096,000 years. The error is

less than two percent. No doubt a better mathematician or

statistician than me could explain the discrepancy.

7 The Boojumase Model

=====================

This is a simple model, deliberately so in order to simplify the

calculations. However it is more complex and closer to the real

situation than the model implied by the naive probability calculation.

The naive model covers the random nature of mutations but it does not

include either the highly non-random process of natural selection or

the ratcheting effect of small changes over the generations in a

population and so gives a misleading result. The boojumase model by

including random mutations, the non-random element of natural

selection and the ratchet effect gives a less misleading result.

The boojumase model is intended as a learning aid. For that reason it

is simplified to remove all calculus and more advanced mathematics.

It is intended for an interested lay audience, not for publication in

Science or Nature.

I have deliberately made life difficult for the model by starting with

the 5% random match between snarkase and boojumase, by allowing only

one amino acid to be effective at each position and by picking a long

interval between significant mutations. This is to avoid criticism

that the model is biased in favour of a short time to evolve the

protein; if anything the model is biased towards a long time to evolve

the protein.

The model is by no means perfect. Possible improvements to it are:

- To improve the calculation of the time taken to spread a beneficial

mutation through the whole population. I tried this myself and got a

figure of 3293 years; not different enough to warrant the extra

complexity and with no effect on the overall result as it is still

less than 4,000 years.

- To take into account sexual reproduction in the spreading of

beneficial mutations.

- Run the exact calculation of tables for more than three mutations

before switching to the AEE.

- Explain the transition from the exact tables to the AEE better than

I have in section 4.2.

- Allow mutations to overlap so a second significant mutation might

occur before the previous mutation has spread through the whole

population. This would allow a more realistic rate of significant

mutations.

- Look at mutation rates in real life and make a better assumption

for the interval between significant mutations. I picked 4000 years

purely to avoid complications with overlapping mutations.

Feel free to take up this model, clean it up and make it a better

reflection of reality. If you do so please bear in mind its purpose

and do not complicate it too much; remember the target audience.

8 Bibliography

==============

Lewis Carroll: Jabberwocky

Lewis Carroll: The Hunting of the Snark

Nov 18, 2011, 11:33:41 AM11/18/11

to

On Nov 18, 10:57 am, rossum <rossu...@coldmail.com> wrote:

> It is some time since I have posted this, so I thought it was time for

> another outing. So, once again, we have ...

>

> rossum

>

> The Evolution of Boojmase

> =========================

[snup]
> It is some time since I have posted this, so I thought it was time for

> another outing. So, once again, we have ...

>

> rossum

>

> The Evolution of Boojmase

> =========================

Allow me to be the first to say: brillig!

Mitchell Coffey

Nov 18, 2011, 11:51:08 AM11/18/11

to

On Fri, 18 Nov 2011 15:57:56 +0000, rossum <ross...@coldmail.com>

wrote:

Here is a photo of the devastating effect boojumase has on what would

otherwise be a normal tree

http://www.treepicturesonline.com/boojum-tree-picture4.jpg

wrote:

otherwise be a normal tree

http://www.treepicturesonline.com/boojum-tree-picture4.jpg

Nov 18, 2011, 6:57:57 PM11/18/11

to

--

John S. Wilkins, Associate, Philosophy, University of Sydney

http://evolvingthoughts.net

But al be that he was a philosophre,

Yet hadde he but litel gold in cofre

Nov 18, 2011, 7:20:22 PM11/18/11

to

rossum <ross...@coldmail.com> wrote:

>It is some time since I have posted this, so I thought it was time for

>another outing. So, once again, we have ...

>rossum

>The Evolution of Boojmase

>=========================

[...]
>It is some time since I have posted this, so I thought it was time for

>another outing. So, once again, we have ...

>rossum

>The Evolution of Boojmase

>=========================

Excellent! Amazingly good!

--

--- Paul J. Gans

Nov 18, 2011, 7:23:19 PM11/18/11

to

On Sat, 19 Nov 2011 10:57:57 +1100, jo...@wilkins.id.au (John S.

Wilkins) wrote:

>Mitchell Coffey <mitchel...@gmail.com> wrote:

>

>> On Nov 18, 10:57 am, rossum <rossu...@coldmail.com> wrote:

>> > It is some time since I have posted this, so I thought it was time for

>> > another outing. So, once again, we have ...

>> >

>> > rossum

>> >

>> > The Evolution of Boojmase

>> > =========================

>> [snup]

>>

>> Allow me to be the first to say: brillig!

>>

>I have to say, it left me in its wabe.

Would it be ever so pedantic to remark that Jabberwocky is contained
Wilkins) wrote:

>Mitchell Coffey <mitchel...@gmail.com> wrote:

>

>> On Nov 18, 10:57 am, rossum <rossu...@coldmail.com> wrote:

>> > It is some time since I have posted this, so I thought it was time for

>> > another outing. So, once again, we have ...

>> >

>> > rossum

>> >

>> > The Evolution of Boojmase

>> > =========================

>> [snup]

>>

>> Allow me to be the first to say: brillig!

>>

>I have to say, it left me in its wabe.

in a work quite separate from the Hunting of the Snark?

Nov 18, 2011, 7:32:54 PM11/18/11

to

On Nov 19, 12:23 am, r norman <r_s_nor...@comcast.net> wrote:

> On Sat, 19 Nov 2011 10:57:57 +1100, j...@wilkins.id.au (John S.

>

>

>

>

>

>

>

>

>

> Wilkins) wrote:

severity; 'it's very rude.'

> On Sat, 19 Nov 2011 10:57:57 +1100, j...@wilkins.id.au (John S.

>

>

>

>

>

>

>

>

>

> Wilkins) wrote:

> >Mitchell Coffey <mitchell.cof...@gmail.com> wrote:

>

> >> On Nov 18, 10:57 am, rossum <rossu...@coldmail.com> wrote:

> >> > It is some time since I have posted this, so I thought it was time for

> >> > another outing. So, once again, we have ...

>

> >> > rossum

>

> >> > The Evolution of Boojmase

> >> > =========================

> >> [snup]

>

> >> Allow me to be the first to say: brillig!

>

> >I have to say, it left me in its wabe.

>

> Would it be ever so pedantic to remark that Jabberwocky is contained

> in a work quite separate from the Hunting of the Snark?

'You should learn not to make personal remarks,' Alice said with some
>

> >> On Nov 18, 10:57 am, rossum <rossu...@coldmail.com> wrote:

> >> > It is some time since I have posted this, so I thought it was time for

> >> > another outing. So, once again, we have ...

>

> >> > rossum

>

> >> > The Evolution of Boojmase

> >> > =========================

> >> [snup]

>

> >> Allow me to be the first to say: brillig!

>

> >I have to say, it left me in its wabe.

>

> Would it be ever so pedantic to remark that Jabberwocky is contained

> in a work quite separate from the Hunting of the Snark?

severity; 'it's very rude.'

Nov 18, 2011, 7:56:07 PM11/18/11

to

On 11/18/2011 6:57 PM, John S. Wilkins wrote:

> Mitchell Coffey<mitchel...@gmail.com> wrote:

>

>> On Nov 18, 10:57 am, rossum<rossu...@coldmail.com> wrote:

>>> It is some time since I have posted this, so I thought it was time for

>>> another outing. So, once again, we have ...

>>>

>>> rossum

>>>

>>> The Evolution of Boojmase

>>> =========================

>> [snup]

>>

>> Allow me to be the first to say: brillig!

>>

> I have to say, it left me in its wabe.

Quite a flight of mimsy.
> Mitchell Coffey<mitchel...@gmail.com> wrote:

>

>> On Nov 18, 10:57 am, rossum<rossu...@coldmail.com> wrote:

>>> It is some time since I have posted this, so I thought it was time for

>>> another outing. So, once again, we have ...

>>>

>>> rossum

>>>

>>> The Evolution of Boojmase

>>> =========================

>> [snup]

>>

>> Allow me to be the first to say: brillig!

>>

> I have to say, it left me in its wabe.

Mitchell

Nov 18, 2011, 8:41:23 PM11/18/11

to

Alice's Adventures in Wonderland (1865)

Facts

Rhyme? And Reason? (also published as Phantasmagoria)

Pillow Problems

Sylvie and Bruno

Sylvie and Bruno Concluded

The Hunting of the Snark (1876)

Three Sunsets and Other Poems

Through the Looking-Glass, and What Alice Found There (includes

"Jabberwocky" and "The Walrus and the Carpenter") (1871)

What the Tortoise Said to Achilles

Also:

Winnie-the-Pooh (1926) (illustrated by E. H. Shepard)

The House at Pooh Corner (1928) (illustrated by E. H. Shepard)

When We Were Very Young

Now We Are Six

Trial by Jury (1875)

The Sorcerer (1877)

H.M.S. Pinafore, or The Lass that Loved a Sailor (1878)

The Pirates of Penzance, or The Slave of Duty (1880)

Patience, or Bunthorne's Bride (1881)

Iolanthe, or The Peer and the Peri (1882)

Princess Ida, or Castle Adamant (1884)

The Mikado, or The Town of Titipu (1885)

Ruddigore, or The Witch's Curse (1887)

The Yeomen of the Guard, or The Merryman and his Maid (1888)

The Gondoliers, or The King of Barataria (1889)

Utopia Limited, or The Flowers of Progress (1893)

The Grand Duke, or The Statutory Duel (1896)

There are a number of minor scriptures, such as those by the Prophets

Kafka (PBUH) and Asimov (PBUH).

Defer!

Nov 18, 2011, 8:46:36 PM11/18/11

to

In article

<4dd13a23-bcd9-4d0c...@r28g2000yqj.googlegroups.com>,

Stuff like this makes me want to outgrabe.

--

It is the nature of the human species to reject what is true but unpleasant

and to embrace what is obviously false but comforting. -- H. L. Mencken

<4dd13a23-bcd9-4d0c...@r28g2000yqj.googlegroups.com>,

--

It is the nature of the human species to reject what is true but unpleasant

and to embrace what is obviously false but comforting. -- H. L. Mencken

Nov 18, 2011, 10:04:59 PM11/18/11

to

On Sat, 19 Nov 2011 12:41:23 +1100, jo...@wilkins.id.au (John S. Wilkins)

wrote in talk.origins:

A very fine collection of scripture.

wrote in talk.origins:

Nov 18, 2011, 10:18:50 PM11/18/11

to

On Sat, 19 Nov 2011 12:41:23 +1100, jo...@wilkins.id.au (John S.

Sorry but my posts was merely corroborative detail, intended to give

artistic verisimilitude to an otherwise bald and unconvincing

narrative.

As to the canon: "Very young" and "Now we are.." were childhood works,

completely assimilated but only half memorized in grade school. The

Penguin "Complete works of Lewis Carroll" was finished in high school,

cover to cover. I never saw "Grand Duke" but did see "Cox and Box"

(only semi-canonical) having been a long time FUMGASS (friend of the

UofM G&S Society).

You forgot Gamow -- "1,2,3 Infinity" and the incomparable "Mr.

Tompkins" books.

artistic verisimilitude to an otherwise bald and unconvincing

narrative.

As to the canon: "Very young" and "Now we are.." were childhood works,

completely assimilated but only half memorized in grade school. The

Penguin "Complete works of Lewis Carroll" was finished in high school,

cover to cover. I never saw "Grand Duke" but did see "Cox and Box"

(only semi-canonical) having been a long time FUMGASS (friend of the

UofM G&S Society).

You forgot Gamow -- "1,2,3 Infinity" and the incomparable "Mr.

Tompkins" books.

Nov 18, 2011, 10:27:22 PM11/18/11

to

Mitchell

Nov 19, 2011, 12:42:47 AM11/19/11

to

should have put Walt Whitman in there as well.

Nov 19, 2011, 12:59:43 AM11/19/11

to

In article <1kazni5.1sj0w961qpm39lN%jo...@wilkins.id.au>,

Out of the Kraken, endlessly Rocking? I'm boggled at your introducing

Whitman here (despite my fondness for him). Somehow, "Crossing Brooklyn

Ferry" and "When Lilacs Last in the Courtyard Bloomed" don't seem to

fit with these others. I suppose the "Do I contradict myself" line might

be commentary on our discussions, but -- huh? --

Whitman here (despite my fondness for him). Somehow, "Crossing Brooklyn

Ferry" and "When Lilacs Last in the Courtyard Bloomed" don't seem to

fit with these others. I suppose the "Do I contradict myself" line might

be commentary on our discussions, but -- huh? --

Nov 19, 2011, 1:12:27 AM11/19/11

to

E.g.,

Has any one supposed it lucky to be born?

I hasten to inform him or her it is just as lucky to die, and I know it.

I pass death with the dying and birth with the new-wash'd babe, and

am not contain'd between my hat and boots

or

I accept Reality and dare not question it,

Materialism first and last imbuing.

Hurrah for positive science! long live exact demonstration!

Fetch stonecrop mixt with cedar and branches of lilac,

This is the lexicographer, this the chemist, this made a grammar of

the old cartouches,

These mariners put the ship through dangerous unknown seas.

This is the geologist, this works with the scalper, and this is a

mathematician.

Gentlemen, to you the first honors always!

Your facts are useful, and yet they are not my dwelling,

I but enter by them to an area of my dwelling.

Nov 19, 2011, 1:31:13 AM11/19/11

to

In article <1kazov5.1gy4g7h5xqf9hN%jo...@wilkins.id.au>,

OK. It certainly is a grab bag of stuff.. :-) I hadn't encountered

that kind of usage (but my philosophy background is of a rather odd

"Chicago School" [no, _not_ the business/economic kind! :-)]) that

stemmed from R. M. Hutchins' notions of what a university was about...

That and the Committee on Social Thought.

that kind of usage (but my philosophy background is of a rather odd

"Chicago School" [no, _not_ the business/economic kind! :-)]) that

stemmed from R. M. Hutchins' notions of what a university was about...

That and the Committee on Social Thought.

Nov 19, 2011, 1:38:23 AM11/19/11

to

Mitchell

Nov 19, 2011, 2:26:49 AM11/19/11

to

Democracy

The flag goes with the foul landscape, and our jargon muffles the drum.

In the great centers we'll nurture the most cynical prostitution. We'll

massacre logical revolts.

In spicy and drenched lands!-- at the service of the most monstrous

exploitations, industrial or military.

Farewell here, no matter where. Conscripts of good will, ours will be a

ferocious philosophy; ignorant as to science, rabid for comfort; and let

the rest of the world croak. This is the real advance. Marching orders,

let's go!

- Arthur Rimbaud, Illuminations

Mitchell

Nov 19, 2011, 8:47:20 AM11/19/11

to

"Mitchell Coffey" <mitchel...@gmail.com> wrote in message

news:4dc435b0-03a2-4b2e...@q16g2000yqn.googlegroups.com:

My toves are slithy.

-- Steven L.

Nov 19, 2011, 10:36:49 AM11/19/11

to

ignoring the possibility that the development might get

stuck at some fitness optimum where no single beneficial

mutation is possible?

Regards,

Karel

Nov 19, 2011, 12:04:33 PM11/19/11

to

On Fri, 18 Nov 2011 22:31:13 -0800, Michael Siemon <mlsi...@sonic.net>

wrote in talk.origins:

Seems like a great program from what I see about it, but the name is a

bit unsettling.

wrote in talk.origins:

bit unsettling.

Nov 19, 2011, 3:02:07 PM11/19/11

to

Nov 19, 2011, 3:22:43 PM11/19/11

to

>

> 7 The effectiveness of a boojumase at digesting boojums is equal to

> the percentage of effective amino acids it contains. Thus since

> normal snarkase has 5% effective amino acids it can digest 5% of

> boojums during their passage through the mome rath's gut. A boojumase

> with 20 effective amino acids would be 20% effective and would digest

> 20% of boojums and so forth.

>

> 8 Each 1% of increased effectiveness of boojumase gives a Mome Rath a

> 1% advantage in reproduction. Similarly a 1% decrease in

> effectiveness will give a 1% decrease in the effectiveness of

> reproduction. This includes the effect of the changed probability of

> the Mome Rath softly and suddenly vanishing away.

>

These are erroroneous, contrary to reality, assumptions. Indeed, this
> 7 The effectiveness of a boojumase at digesting boojums is equal to

> the percentage of effective amino acids it contains. Thus since

> normal snarkase has 5% effective amino acids it can digest 5% of

> boojums during their passage through the mome rath's gut. A boojumase

> with 20 effective amino acids would be 20% effective and would digest

> 20% of boojums and so forth.

>

> 8 Each 1% of increased effectiveness of boojumase gives a Mome Rath a

> 1% advantage in reproduction. Similarly a 1% decrease in

> effectiveness will give a 1% decrease in the effectiveness of

> reproduction. This includes the effect of the changed probability of

> the Mome Rath softly and suddenly vanishing away.

>

error is fundamental to much of the theory concerning evolutionary

mechanisms. There is no way that one takes a protein for one metabolic

process, makes a single amino acid change and gets a 1% increase in a

different metabolic process. To get an active site on a protein there is

little leeway on changes to that protein; besides requiring effective

amino acids at the active site, most other amino acids must contribute

to a correct folding of the protein to get the active site.

This notion of gradualism is a fantasy.

Nov 20, 2011, 8:05:17 AM11/20/11

to

On Sat, 19 Nov 2011 12:41:23 +1100, jo...@wilkins.id.au (John S.

There is only one true and Holy Scripture, completely free from error:

The Bellman's Map

-----------------

He had bought a large map representing the sea,

Without the least vestige of land:

And the crew were much pleased when they found it to be

A map they could all understand.

"What’s the good of Mercator’s North Poles and Equators,

Tropics, Zones, and Meridian Lines?"

So the Bellman would cry: and the crew would reply

"They are merely conventional signs!

"Other maps are such shapes, with their islands and capes!

But we’ve got our brave Bellman to thank"

(So the crew would protest) "that he’s bought us the best -

A perfect and absolute blank!"

rosuum

The Bellman's Map

-----------------

He had bought a large map representing the sea,

Without the least vestige of land:

And the crew were much pleased when they found it to be

A map they could all understand.

"What’s the good of Mercator’s North Poles and Equators,

Tropics, Zones, and Meridian Lines?"

So the Bellman would cry: and the crew would reply

"They are merely conventional signs!

"Other maps are such shapes, with their islands and capes!

But we’ve got our brave Bellman to thank"

(So the crew would protest) "that he’s bought us the best -

A perfect and absolute blank!"

rosuum

Nov 20, 2011, 8:09:14 AM11/20/11

to

On Sat, 19 Nov 2011 07:36:49 -0800 (PST), Karel

<GCPAXS...@spammotel.com> wrote:

>Interesting, no, very interesting as this is, aren't you

>ignoring the possibility that the development might get

>stuck at some fitness optimum where no single beneficial

>mutation is possible?

>

>Regards,

>

>Karel

This is a simple teaching exercise, intended to illustrate the
<GCPAXS...@spammotel.com> wrote:

>Interesting, no, very interesting as this is, aren't you

>ignoring the possibility that the development might get

>stuck at some fitness optimum where no single beneficial

>mutation is possible?

>

>Regards,

>

>Karel

differentce between the typical creationist "tornado in a junkyard"

scenario and a simple calculation that includes the effects of natural

selection.

In real life, you are right of course. Evolution does get suck at

local optima; it even remains on those local optima when they are no

longer optimal. Think of recurrent laryngeal nerve which was

optimally routed when we were fish, but now has a sub-optimal route

because it has kept to the one optimal route.

rossum

Nov 20, 2011, 8:12:49 AM11/20/11

to

On Sat, 19 Nov 2011 12:22:43 -0800, rmj <glennaRe...@jps.net>

wrote:

I said that this was an illustration of the incorrectness of "tornado

in a junkyard" models that omit natural selection. Even YECs accept

the validity of micro-evolution, and almost all of micro-evolution is

gradual. Minor tweaks spreading through a population.

Have you looked at Yockey's calculation of the number of possible

Cytochrome-C's? 2.3 x 10^93 possible ways to make a working

Cytochrome-C. There is plenty of gradualism allowed ithin that number

of options.

rossum

wrote:

in a junkyard" models that omit natural selection. Even YECs accept

the validity of micro-evolution, and almost all of micro-evolution is

gradual. Minor tweaks spreading through a population.

Have you looked at Yockey's calculation of the number of possible

Cytochrome-C's? 2.3 x 10^93 possible ways to make a working

Cytochrome-C. There is plenty of gradualism allowed ithin that number

of options.

rossum

Nov 20, 2011, 9:04:56 AM11/20/11

to

On 20 nov, 14:09, rossum <rossu...@coldmail.com> wrote:

> On Sat, 19 Nov 2011 07:36:49 -0800 (PST), Karel

>

> On Sat, 19 Nov 2011 07:36:49 -0800 (PST), Karel

>

it certainly worked for me. Thank you!

Regards,

Karel

Nov 20, 2011, 3:32:50 PM11/20/11

to

Nov 20, 2011, 3:45:59 PM11/20/11

to

of GBShaw's prefaces to his plays.

Nov 20, 2011, 11:17:36 PM11/20/11

to

no probable, possible shadow of doubt,

no possible doubt whatever.

--

Mark Isaak eciton (at) curioustaxonomy (dot) net

"It is certain, from experience, that the smallest grain of natural

honesty and benevolence has more effect on men's conduct, than the most

pompous views suggested by theological theories and systems." - D. Hume

Nov 21, 2011, 1:41:05 AM11/21/11

to

number of assumptions. Still, if one accepts is number as fairly

accurate, it is relatively miniscule. For a 100 amino acid protein (like

cytochrome c), there are 20^100 possible amino acid sequences. Now my

math skills are not solid, but that is of the order of 10^130. So

compare 10^93 to 10^130.

There is another problem with your model. Just because four or five

amino acid changes may increase effectiveness, does not mean that there

is another amino acid change that can increase effectiveness. How does

your model account for dead ends, lines that can get to, say, 20%

efficiency, but where there is no route to greater efficiency without

undoing what changes had occurred?

Nov 21, 2011, 12:50:42 PM11/21/11

to

On Sun, 20 Nov 2011 22:41:05 -0800, rmj <glennaRe...@jps.net>

wrote:

Yockey's calculations show that the naive 10^130 figure is wrong by a

factor of 10^93. Of course the 10^130 figure includes all possible

functional proteins of that length, a figure considerably higher than

10^93. If a protein is useful then natural selection will tend to

increase its frequency in the population. It may not be useful as a

Cytochrome-C, but it may be useful as something else.

>

>There is another problem with your model. Just because four or five

>amino acid changes may increase effectiveness, does not mean that there

>is another amino acid change that can increase effectiveness. How does

>your model account for dead ends, lines that can get to, say, 20%

>efficiency, but where there is no route to greater efficiency without

>undoing what changes had occurred?

My model was deliberately kept simple. It only needed to be simple

because the creationist "tornado in a junkyard", your 10^130 is itself

grossly oversimplified and not a good model of evolution.

By all means add the possibility of getting 'caught' to my model. You

will need to explain the changes you are making and to do the forward

calculations yourself.

As I said, this is a simplified teachimg model, not an accurate model

of evolution.

rossum

wrote:

factor of 10^93. Of course the 10^130 figure includes all possible

functional proteins of that length, a figure considerably higher than

10^93. If a protein is useful then natural selection will tend to

increase its frequency in the population. It may not be useful as a

Cytochrome-C, but it may be useful as something else.

>

>There is another problem with your model. Just because four or five

>amino acid changes may increase effectiveness, does not mean that there

>is another amino acid change that can increase effectiveness. How does

>your model account for dead ends, lines that can get to, say, 20%

>efficiency, but where there is no route to greater efficiency without

>undoing what changes had occurred?

because the creationist "tornado in a junkyard", your 10^130 is itself

grossly oversimplified and not a good model of evolution.

By all means add the possibility of getting 'caught' to my model. You

will need to explain the changes you are making and to do the forward

calculations yourself.

As I said, this is a simplified teachimg model, not an accurate model

of evolution.

rossum

Nov 23, 2011, 10:45:29 AM11/23/11

to

>

>>

>> There is another problem with your model. Just because four or five

>> amino acid changes may increase effectiveness, does not mean that there

>> is another amino acid change that can increase effectiveness. How does

>> your model account for dead ends, lines that can get to, say, 20%

>> efficiency, but where there is no route to greater efficiency without

>> undoing what changes had occurred?

> My model was deliberately kept simple. It only needed to be simple

> because the creationist "tornado in a junkyard", your 10^130 is itself

> grossly oversimplified and not a good model of evolution.

Then you admit you have chosen those assumptions because you have an agenda.
>>

>> There is another problem with your model. Just because four or five

>> amino acid changes may increase effectiveness, does not mean that there

>> is another amino acid change that can increase effectiveness. How does

>> your model account for dead ends, lines that can get to, say, 20%

>> efficiency, but where there is no route to greater efficiency without

>> undoing what changes had occurred?

> My model was deliberately kept simple. It only needed to be simple

> because the creationist "tornado in a junkyard", your 10^130 is itself

> grossly oversimplified and not a good model of evolution.

>

> By all means add the possibility of getting 'caught' to my model. You

> will need to explain the changes you are making and to do the forward

> calculations yourself.

>

> As I said, this is a simplified teachimg model, not an accurate model

> of evolution.

>

> rossum

>

Nov 23, 2011, 1:04:32 PM11/23/11

to

On Wed, 23 Nov 2011 07:45:29 -0800, rmj <glennaRe...@jps.net>

You are free to read Yockey's work and to point out his errors. As to

the functionality of random protiens see

http://amesteam.arc.nasa.gov/Research/proteins.html

These are not assertions and assumptions, they are considered results

from scientific experiments. Your creationist sources are lying to

you.

>>

>>>

>>> There is another problem with your model. Just because four or five

>>> amino acid changes may increase effectiveness, does not mean that there

>>> is another amino acid change that can increase effectiveness. How does

>>> your model account for dead ends, lines that can get to, say, 20%

>>> efficiency, but where there is no route to greater efficiency without

>>> undoing what changes had occurred?

>> My model was deliberately kept simple. It only needed to be simple

>> because the creationist "tornado in a junkyard", your 10^130 is itself

>> grossly oversimplified and not a good model of evolution.

>

>Then you admit you have chosen those assumptions because you have an agenda.

I am building a simple teaching model. That is what I said in my OP.

Didn't you read it?

>

>>

>> By all means add the possibility of getting 'caught' to my model. You

>> will need to explain the changes you are making and to do the forward

>> calculations yourself.

>>

>> As I said, this is a simplified teachimg model, not an accurate model

>> of evolution.

>

>I would that teachers attempt to place honesty first.

You don't start a First Grade Math class on Tensor Algebra. One of

the skills required of a teacher is to ensure that the lesson is at an

appropriate level for the pupils in the classroom. Do you have a

problem with that?

Is a Sunday School teacher who fails to teach First Graders about the

difference between 'homoousion' and 'homoiousion', and all the Greek

grammar neded to understand that differeence, being dishonest?

A full mathematical model of evolution requires calculus. My model is

intended for people who may not have a sufficient understanding of

calculus. My model is reasonably close to the real thing, and is

sufficient to show that the creationist model is grossly in error.

If you want teachers to be honest, then stop them trying to push the

creationist "tornado in a junkyard" model. That is far more dishonest

than my Boojumase model. Didn't someone say something about motes and

beams?

rossum

the functionality of random protiens see

http://amesteam.arc.nasa.gov/Research/proteins.html

These are not assertions and assumptions, they are considered results

from scientific experiments. Your creationist sources are lying to

you.

>>

>>>

>>> There is another problem with your model. Just because four or five

>>> amino acid changes may increase effectiveness, does not mean that there

>>> is another amino acid change that can increase effectiveness. How does

>>> your model account for dead ends, lines that can get to, say, 20%

>>> efficiency, but where there is no route to greater efficiency without

>>> undoing what changes had occurred?

>> My model was deliberately kept simple. It only needed to be simple

>> because the creationist "tornado in a junkyard", your 10^130 is itself

>> grossly oversimplified and not a good model of evolution.

>

>Then you admit you have chosen those assumptions because you have an agenda.

Didn't you read it?

>

>>

>> By all means add the possibility of getting 'caught' to my model. You

>> will need to explain the changes you are making and to do the forward

>> calculations yourself.

>>

>> As I said, this is a simplified teachimg model, not an accurate model

>> of evolution.

>

>I would that teachers attempt to place honesty first.

the skills required of a teacher is to ensure that the lesson is at an

appropriate level for the pupils in the classroom. Do you have a

problem with that?

Is a Sunday School teacher who fails to teach First Graders about the

difference between 'homoousion' and 'homoiousion', and all the Greek

grammar neded to understand that differeence, being dishonest?

A full mathematical model of evolution requires calculus. My model is

intended for people who may not have a sufficient understanding of

calculus. My model is reasonably close to the real thing, and is

sufficient to show that the creationist model is grossly in error.

If you want teachers to be honest, then stop them trying to push the

creationist "tornado in a junkyard" model. That is far more dishonest

than my Boojumase model. Didn't someone say something about motes and

beams?

rossum

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