Tag Archives: Research

New software calculates the probability of generating functional proteins by chance

Apologetics and the progress of science
Apologetics and the progress of science

Here’s an article sent to me by JoeCoder about a new computer program written by Kirk Durston.

About Kirk:

Kirk Durston is a scientist, a philosopher, and a clergyman with a Ph.D. in Biophysics, an M.A. in Philosophy, a B.Sc. in Mechanical Engineering, and a B.Sc. in Physics. His work involves a significant amount of time thinking, writing and speaking about the interaction of science, theology and philosophy within the context of authentic Christianity. He has been married for 34 years to Patti and they have six children and three grandchildren. He enjoys landscape photography, antiques of various types, wilderness canoeing and camping, fly fishing, amateur astronomy, reading, music, playing the saxophone (alto), and enjoying family and friends.

Kirk grew up on a cattle and grain farm in central Manitoba, Canada, where he spent countless hours wandering around on his own in the forest as a young boy, fascinated with the plants and animals that are native to that region of the province. Throughout his teen years he spent six days a week in the summer working as a farm hand with cattle and grain. He left his father’s farm at the age of 19 to go to university.

Canada? Can anything good come out of Canada? Oh well, at least he’s not from Scotland. Anyway, on to the research, that’s what we care about. Code!

Summary of the article:

  • Biological life requires proteins
  • Proteins are sequences of amino acids, chained together
  • the order of amino acids determines whether the sequence has biological function
  • sequences that have biological function are rare, compared to the total number of possible sequences
  • Durston wrote a program to calculate the number of the probability of getting a functional sequence by random chance
  • The probability for getting a functional protein by chance is incredibly low

With that said, we can understand what he wrote:

This program can compute an upper limit for the probability of obtaining a protein family from a wealth of actual data contained in the Pfam database. The first step computes the lower limit for the functional complexity or functional information required to code for a particular protein family, using a method published by Durston et al. This value for I(Ex) can then be plugged into an equation published by Hazen et al. in order to solve the probability M(Ex)/N of ‘finding’ a functional sequence in a single trial.

I downloaded 3,751 aligned sequences for the Ribosomal S7 domain, part of a universal protein essential for all life. When the data was run through the program, it revealed that the lower limit for the amount of functional information required to code for this domain is 332 Fits (Functional Bits). The extreme upper limit for the number of sequences that might be functional for this domain is around 10^92. In a single trial, the probability of obtaining a sequence that would be functional for the Ribosomal S7 domain is 1 chance in 10^100 … and this is only for a 148 amino acid structural domain, much smaller than an average protein.

For another example, I downloaded 4,986 aligned sequences for the ABC-3 family of proteins and ran it through the program. The results indicate that the probability of obtaining, in a single trial, a functional ABC-3 sequence is around 1 chance in 10^128. This method ignores pairwise and higher order relationships within the sequence that would vastly limit the number of functional sequences by many orders of magnitude, reducing the probability even further by many orders of magnitude – so this gives us a best-case estimate.

There are only about 10^80 particles in the entire physical universe – 10^85 at the most. These are long odds. But maybe if we expand the probabilistic resources by buying more slot machines, and we pull the slot machine lever at much faster rate… can we win the jackpot then?

Nope:

What are the implications of these results, obtained from actual data, for the fundamental prediction of neo-Darwinian theory mentioned above? If we assume 10^30 life forms with a fast replication rate of 30 minutes and a huge genome with a very high mutation rate over a period of 10 billion years, an extreme upper limit for the total number of mutations for all of life’s history would be around 10^43. Unfortunately, a protein domain such as Ribosomal S7 would require a minimum average of 10^100 trials, about 10^57 trials more than the entire theoretical history of life could provide – and this is only for one domain. Forget about ‘finding’ an average sized protein, not to mention thousands.

So even if you have lots of probabilistic resources, and lots of time, you’re still not going to get your protein.

Compare these numbers with the 1 in 10^77 number that I posted about yesterday from Doug Axe. There is just no way to account for proteins if there is no intelligent agent to place the amino acids in sequence. When it comes to writing code, writing blog posts, writing music, or placing Scrabble letters, you need an intelligence. Sequencing amino acids into proteins? You need an intelligence.

First openly gay Episcopal bishop to divorce same-sex partner

This is an Associated Press article, so it is extremely liberal and sympathetic to the gay bishop. (H/T Tom)

Excerpt:

The first openly gay Episcopal bishop, who became a symbol for gay rights far beyond the church while deeply dividing the world’s Anglicans, plans to divorce his husband.

[…]Robinson, 66, had been married to a woman and had two children before he and his wife divorced. He and Andrew had been partners for more than a decade when Robinson was elected to lead the New Hampshire Diocese. The two men were joined in a 2008 civil union in New Hampshire, which became a legal marriage when the state recognized gay marriage two years later.

[…]Robinson was… widely celebrated as a pioneer for gay rights, became an advocate for gay marriage and was the subject of several books and a documentary about Christianity, the Bible and same-sex relationships. He delivered the benediction at the opening 2009 inaugural event for President Barack Obama and, after retirement, became a senior fellow at the Center for American Progress, a Democratic think tank with close ties to the White House.

The interesting thing about this is that although Americans have been fed a steady diet of propaganda from Hollywood to make us think that gay relationships are stable, the reality is that they are NOT stable.

Let’s take a look at the data

Consider this post from The Public Discourse which explains that there are few stable, long-lived gay relationships – even the ones with children.

Excerpt:

The [NFSS] study found that the children who were raised by a gay or lesbian parent as little as 15 years ago were usually conceived within a heterosexual marriage, which then underwent divorce or separation, leaving the child with a single parent. That parent then had at least one same-sex romantic relationship, sometimes outside of the child’s home, sometimes within it. To be more specific, among the respondents who said their mother had a same-sex romantic relationship, a minority, 23%, said they had spent at least three years living in the same household with both their mother and her romantic partner. Only 2 out of the 15,000 screened spent a span of 18 years with the same two mothers. Among those who said their father had had a same-sex relationship, 1.1% of children reported spending at least three years together with both men.

This strongly suggests that the parents’ same-sex relationships were often short-lived, a finding consistent with the broader research on elevated levels of instability among same-sex romantic partners. For example, a recent 2012 study of same-sex couples in Great Britain finds that gay and lesbian cohabiting couples are more likely to separate than heterosexual couples. A 2006 study of same sex marriages in Norway and Sweden found that “divorce risk levels are considerably higher in same-sex marriages” such that Swedish lesbian couples are more than three times as likely to divorce as heterosexual couples, and Swedish gay couples are 1.35 times more likely to divorce (net of controls). Timothy Biblarz and Judith Stacey, two of the most outspoken advocates for same-sex marriage in the U.S. academy, acknowledge that there is more instability among lesbian parents.

Therefore, while critics of the NFSS have faulted it for lacking comparisons between children of IBFs and the children of committed and intact gay or lesbian couples, this was attempted, but was not feasible. Despite drawing from a large, representative sample of the U.S. population, and despite using screening tactics designed to boost the number of respondents who reported having had a parent in a same-sex relationship, a very small segment reported having been parented by the same two women or two men for a minimum of three years. Although there is much speculation that today there are large numbers of same-sex couples in the U.S. who are providing a stable, long-term parenting relationship for their children, no studies based upon large, random samples of the U.S. population have been published that show this to be true, and the above-cited studies of different nations show that on average, same-sex couple relationships are more short-lived than those of opposite-sex couples.

I think this is an important point to make – and it’s consistent with the research from previous studies. The bottom line is that gay marriage is another step on the path towards making marriage about the needs and feelings of adults. In natural marriage, parents are concerned about how breaking up will affect their children – so thy have a reason to stay together and work conflicts out. The needs of the adults are secondary to the needs of the children. But in gay marriage, there is no such constraint. The children are not related biologically to both partners, and so that protection is not in place. Now that gay marriage is legalized, we should understand that children will be getting a lot less stability, and that’s in addition to being deprived of their biological mother and father.

Is the EPA paying researchers to produce only the results they want?

Atmospheric temperature measurements though April 2015
Atmospheric temperature measurements though April 2015

This remarkable story is from the Daily Signal.

It says:

Researchers from Harvard University, Syracuse University and four other institutions used climate models to predict the impact the EPA’s proposed carbon emissions reductions would have on human health. And not surprisingly, it turned out the government’s plan was not just among the options that would produce positive results but was, in fact, the best way to achieve the goals.

But there was a line in this story that sets it apart. Jonathan Buonocore, a research fellow at Harvard’s Center for Health and the Global Environment, told U.S. News the EPA did not participate in the study or interact with its authors.

But it seems the agency did participate and did interact with the authors.

The chain of emails went back and forth as the researchers and the agency both sought to add participants to the call. The fact the research showed precisely what the government wanted it to and that the government’s own proposal, when mimicked by researchers, produced the best results further raise suspicion.

[…]The scientists who produce this government-favored research not only have begun to cash in at taxpayers’ expense, but they’ve also begun to ask the agency for help with fundraising.

The study’s authors got about $45 million in research grants from the EPA, and that is taxpayer’s money.

But surely scientists who are critical of bigger government receive the same government-funding and support, right? After all, research is about truth, and the government just funds research that is truth-focused, right?

Not so much:

Willie Soon, an astrophysicist with the Harvard-Smithsonian Center for Astrophysics, co-authored a paper published in January that found the models used in the UN’s Intergovernmental Panel on Climate Change are laced with mathematical errors. Soon then endured an avalanche of criticism of his funding sources and implications he had shaped his findings to please them.

It mattered not that he got only about $60,000 per year from the one “compromised” source or that the compromised source was the Smithsonian or that he had not known where the Smithsonian got the money it paid him.

Then, a few days after the New York Times piece on Soon appeared, Congress got into the act. Rep. Raul Grijalva, D-Ariz., ranking minority member on the House Natural Resources Committee, sent letters to seven universities asking for documents on climate change research connected with scientific skeptics who have questioned the premise of anthropogenic (man-made) global warming.

This was followed by a letter from Sens. Edward J. Markey, D-Mass., Barbara Boxer, D-Calif., and Sheldon Whitehouse, D-R.I., to 100 fossil fuel companies, trade groups, and other outfits “to determine whether they are funding scientific studies designed to confuse the public and avoid taking action to cut carbon pollution, and whether the funded scientists fail to disclose the sources of their funding in scientific publications or in testimony to legislators.”

Indeed, the deck remains stacked against those who dare to stray from the government message on global warming, and the conflicts of interest seem concentrated on the researchers and scientists who accept government money, according to William Happer, a professor of physics at Princeton University.

“Unless you accept the alarmist position and the dictates of the [Obama] administration, you cannot typically receive government funding,” said Happer.

It’s no wonder that so many Republicans, myself included, put the EPA in the list of Departments we would abolish. For me it’s the Department of Education, the EPA, the Department of Energy and IRS. Just get rid of the public sector bureaucracy at the federal level and push it down to the state and local levels. And privatize as much of it as possible.

Domestic violence rates are higher for homosexual couples than for heterosexual couples

Marriage and family
Marriage and family

From the left-leaning Atlantic Monthly.

Excerpt:

Data on the rates of same-sex partner abuse have only become available in recent years. Even today, many of the statistics and materials on domestic violence put out by organizations like the Center for Disease Control and the Department of Justice still focus exclusively on heterosexual relationships, and specifically heterosexual women. While the CDC does provide some resources on its website for the LGBT population, the vast majority of the information is targeted at women.  Materials provided by the CDC for violence prevention and survivor empowerment prominently feature women in their statistics and photographs.

In 2013, the CDC released the results of a 2010 study on victimization by sexual orientation, and admitted that “little is known about the national prevalence of intimate partner violence, sexual violence, and stalking among lesbian, gay, and bisexual women and men in the United States.” The report found that bisexual women had an overwhelming prevalence of violent partners in their lives: 75 percent had been with a violent partner, as opposed to 46 percent of lesbian women and 43 percent of straight women. For bisexual men, that number was 47 percent. For gay men, it was 40 percent, and 21 percent for straight men.

The most recent statistics available on same-sex intimate partner violence from the National Coalition of Anti-Violence Programs, which focuses on LGBT relationships, reported 21 incidents of intimate partner homicides in the LGBT community, the highest ever. Nearly half of them were gay men and, for the second year in a row, the majority of survivors were people of color—62 percent.

In 2012, NCAVP programs around the country received 2,679 reports of intimate partner violence, a decrease of around 32 percent from 2011. However the report noted that many of the NCAVP’s member organizations were operating at decreased capacity due to limiting the number of cases they were able to take. The report said that excluding data from organizations, there was actually a 29 percent increase in reports of violence from 2011 to 2012.

That article comes from a source with a very clear pro-gay-agenda bias, so let’s take a look at an article from the Family Research Council to balance it out. They rely on mainstream data sources as well, like the CDC, the DOJ, the US Census, etc.

Excerpt:

A study in the Journal of Interpersonal Violence examined conflict and violence in lesbian relationships. The researchers found that 90 percent of the lesbians surveyed had been recipients of one or more acts of verbal aggression from their intimate partners during the year prior to this study, with 31 percent reporting one or more incidents of physical abuse.[69]

In a survey of 1,099 lesbians, the Journal of Social Service Research found that “slightly more than half of the [lesbians] reported that they had been abused by a female lover/partner. The most frequently indicated forms of abuse were verbal/emotional/psychological abuse and combined physical-psychological abuse.”[70]

In their book Men Who Beat the Men Who Love Them: Battered Gay Men and Domestic Violence,D. Island and P. Letellier report that “the incidence of domestic violence among gay men is nearly double that in the heterosexual population.”[71]

[…]Homosexual and lesbian relationships are far more violent than are traditional married households:

The Bureau of Justice Statistics (U.S. Department of Justice) reports that married women in traditional families experience the lowest rate of violence compared with women in other types of relationships.[72]

A report by the Medical Institute for Sexual Health concurred,

It should be noted that most studies of family violence do not differentiate between married and unmarried partner status. Studies that do make these distinctions have found that marriage relationships tend to have the least intimate partner violence when compared to cohabiting or dating relationships.[73]

In lesbian relationships, the rate of domestic violence is extremely high, from 17% to 45%, depending on the study. I do think that men exert a calming influence on women’s emotions, helping them to channel their feelings into words and reasoned arguments. That short-circuits the tendency toward violent outbursts. That’s why I urge men, if they must marry, to practice disagreeing and debating with women before the marriage is actualized. You need to find out what this other person does in a conflict situation before you commit to her for life.

Physicist Frank Tipler on the usefulness of refereed journals, then and now

I really enjoyed this episode of the ID the Future podcast.

Description:

Is the only good science peer-reviewed science? Are there other avenues to present important scientific work? On this episode of ID The Future, Professor of Mathematics Dr. Frank Tipler discusses the pros and cons of peer review and refereed journals. More than fifty peer-reviewed papers discussing intelligent design have been published, but critics of the theory still proclaim a lack of peer-reviewed work as an argument. Listen in as Tipler shows how things have changed with the peer review process and what we can do about it.

About the speaker:

Frank Tipler was born and raised in Andalusia, Alabama. His first science project was a letter written in kindergarten to Werner von Braun, whose plans to launch the first earth satellite were then being publicized. Von Braun’s secretary replied, regretting he had no rocket fuel for Tipler as requested. By age five, he knew he wanted to be an astrophysicist. But he’s always been a polymath, reading widely across disciplines and into the history of science and theology. After graduating from MIT and the University of Maryland, he did postdoctoral work at Oxford and Berkeley, before arriving at Tulane in 1981.

William Lane Craig often cites a book by two physicists named “Barrow and Tipler” called “The Anthropic Cosmological Principle” (Oxford University Press, 1988) in his debates to support the fine-tuning argument.  This Tipler is that Tipler! Dr. Tipler is a master of the physics of cosmology and fine-tuning. However, I definitely disagree with him on some of his ideas.

The MP3 file is here. (17 minutes)

Topics:

  • the changing nature of refereed journals and peer-review
  • previously, the refereed journals were more about communication
  • now, ideas are not taken seriously unless they are published in these journals
  • the problem is that referees can be motivated by ideological concerns
  • before, an obscure patent official named Einstein submitted a physics paper and it was published
  • now, an uncredited person would not be able to have a brilliant paper published like that
  • today, there are so many scientists that many more papers are submitted
  • although it restricts BAD ideas, it can also end up censoring NEW ideas
  • the problem is that any really brilliant idea has to go against the prevailing consensus
  • peer-review may actually be holding back the progress of science by censoring NEW ideas
  • some referees are motivated to censor ideas that undercut their reputation and prestige
  • Dr. Tipler was told to remove references to intelligent design before one of his papers would be published
  • how scientists with NEW ideas can bypass the system of refereed journals when they are censored
  • peer-review has value when it finds errors, but not when it suppresses new ideas

I think this one is a must listen. I like to refer to peer-reviewed evidence when arguing, but it’s not perfect, for sure.